Drug Discovery Links

Click HERE to return to the Division of Medicinal Chemistry Homepage

An annotated list of useful links prepared by Jeff Zablocki and Hugh Genin of CV Therapeutics for drug discovery and medicinal chemistry. Please note that a list such as this one cannot be comprehensive, or even 100% up-to-date, though we will try our best. Also note that annotations are taken from the websites themselves where possible.

Databases

 

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Drugs

 

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Center for Drug Evaluation and Research (CDER) at the U.S. FDA

Drugs@FDA  online Free! 
A catalog of FDA approved drug products, including approved and tentatively approved prescription, over-the-counter, and discontinued drugs; drug approval letters, labels, and review packages.

The Orange Book at the U.S. FDA  online Free! 
Approved Drug Products with Therapeutic Equivalence Evaluations

United States Food and Drug Administration (FDA)

Literature

 

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Beilstein - see Crossfire Beilstein

Chemical Abstracts Service (CAS) 
We provide pathways to published research in the world's journal and patent literature - virtually everything relevant to chemistry plus a wealth of information in the life sciences and a wide range of other scientific disciplines back to the beginning of the 20th century. Offerings include:

SciFinder
A research tool that allows you to access the world's largest collection of biochemical, chemical, chemical engineering, medical, and other related information.

STN
STN International connects scientists, engineers and anyone who needs technical information to the world's most complete and authoritative databases.

ScienceIP
Science IP provides fast, accurate, and comprehensive searches of the worldâs scientific and patent literature.

ChemPort
ChemPort® links users of SciFinder®, STN®, and other electronic CAS products to articles from more than 6700 electronic journals from nearly 280 participating publishers - at no additional charge! It also provides links to electronic patent documents from the USPTO, esp@cenet, and MicroPatent®.

Crossfire Beilstein - see entry under Databases

Journal Names & Abbreviations
List of common chemistry journals and their abbreviations, from UBC libraries.

Journals Of Interest
Annals of Improbable Research
Research that makes people LAUGH and then THINK.

Archiv der Pharmazie - Chemistry in Life Sciences
An international journal devoted to research and development in all fields of pharmaceutical and medicinal chemistry. Emphasis is put on papers combining synthetic organic chemistry, structural biology, molecular modelling, bioorganic chemistry, natural products chemistry, biochemistry or analytical methods with pharmaceutical or medicinal aspects such as biological activity.

Biochemical and Biophysical Research Communications
Research Areas now include: Biochemistry; Biophysics; Cell Biology; Developmental Biology; Immunology; Molecular Biology; Neurobiology; Plant Biology; Proteomic.

Biochemical Pharmacology
All areas of the interaction of drugs and nontherapeutic xenobiotics with biological systems are represented in the journal including, but not limited to, cancer chemotherapy, neuropharmacology, inflammation/immunopharmacology, antimicrobials, behavioral, respiratory, gastrointestinal, cardiovascular, and endocrine pharmacology and toxicology.

Biochemistry
Covers structure, function, and regulation of biologically active molecules; gene structure and expression; biochemical mechanisms; protein biosynthesis; protein folding; membrane structure-function relationships; bioenergetics; and immunochemistry.

Bioinformatics
Its main focus is on new developments in genome bioinformatics and computational biology.

Bioorganic and Medicinal Chemistry
An international forum for the publication of full original research papers and critical reviews on molecular interactions in key biological targets such as receptors, channels, enzymes, nucleotides, lipids and saccharides.

Bioorganic and Medicinal Chemistry Letters
Presents preliminary experimental or theoretical research results of outstanding significance and timeliness on all aspects of science at the interface of chemistry and biology and on major advances in drug design and development.

Biophysical Journal
Publishes original articles, letters and reviews on biophysical topics, emphasizing the molecular and cellular aspects of biology.

Current Pharmaceutical Design
Publishes timely in-depth reviews covering all aspects of current research in rational drug design. Each issue is devoted to a single major therapeutic area.

Current Topics in Medicinal Chemistry
The scope of Current Topics in Medicinal Chemistry will cover all areas of medicinal chemistry, including current developments in rational drug design, synthetic chemistry, bioorganic chemistry, high-throughput screening, combinatorial chemistry, compound diversity measurements, drug absorption, drug distribution, metabolism, new and emerging drug targets, natural products, pharmacogenomics, and structure-activity relationships.

Doklady Biochemistry and Biophysics
A journal containing English translations of current Russian research from the biochemistry and biophysics sections of the Doklady akademii nauk (Proceedings of the Russian Academy of Sciences).

Drug Development Research
The journal publishes original research articles on medicinal chemistry, pharmacology, biotechnology and biopharmaceuticals, toxicology, and drug delivery, formulation, and pharmacokinetics. The journal welcomes manuscripts on new compounds and technologies in all areas focused on human therapeutics, as well as global management, health care policy, and regulatory issues involving the drug discovery and development process.

Drug Discovery Today
Coverage includes: Novel therapeutic strategies; High-throughput screening; Therapeutic targets; Combinatorial chemistry, parallel synthesis and library design; Drug delivery; ADME/Tox; Advances in key compound classes and therapeutic areas; Genomics and proteomics; Automation and technology; Virtual chemistry; Informatics; Business strategy; Clinical trials; and other aspects of drug discovery.

Drug Metabolism and Disposition
Articles provide experimental results from in vitro and in vivo systems that bring you significant and original information on metabolism and disposition of endogenous and exogenous compounds, including pharmacologic agents and environmental chemicals.

The EMBO Journal
The journal encourages submission of articles in the areas of development, immunology, neuroscience, plant biology, structural biology, genomic & computational biology, genome stability & dynamics, chromatin & transcription, RNA, proteins, cellular metabolism, signal transduction, cell cycle, differentiation & death, membranes & transport, cell & tissue architecture, microbiology & pathogens, and molecular biology of disease.

Endocrine Reviews
Endocrine Reviews publishes bimonthly comprehensive, authoritative, and timely review articles balancing both experimental and clinical endocrinology themes and crystallizing the most significant clinical experience and current research in endocrinology and related areas such as cell biology, immunology, pharmacology, genetics, molecular biology, neuroscience, reproductive medicine, and pediatric endocrinology.

Endocrinology
Publishes 6,000 pages annually of the highest quality original work ranging from subcellular mechanisms to whole animal physiology. Topics include bone and mineral; growth factors; reproductive/steroids; neuroendocrinology/signal transduction; thyroid; and physiology.

European Journal of Biochemistry
FEBS Journal is dedicated to the rapid publication of full-length research papers and reviews in all areas of the molecular life sciences. The broad aims and scope include the growing points of bioinformatics, genomics and proteomics, molecular cell biology and the molecular biology of disease, systems biology and nanoscience.

Genes & Development
Publishes high-quality research papers of broad general interest and biological significance in the areas of molecular biology, molecular genetics, and related fields.

Genomics
The goal of Genomics is to promote the understanding of the structure, function, and evolution of genomes in all kingdoms of life and the application of genome sciences and technologies to challenging problems in biology and medicine.

Investigational Drugs Journal (IDrugs)
A monthly review journal that saves you time and money by bringing you reports from the most noteworthy and topical meetings happening around the world.

Journal of Biological Chemistry
The JOURNAL publishes papers based on original research that are judged, after editorial review, to make a novel and important contribution to the understanding of any area of biochemistry or molecular biology.

Journal of Computer-Aided Molecular Design
The scope of the journal encompasses papers which report new and original research and applications in the following areas: theoretical chemistry; computational chemistry; computer and molecular graphics; molecular modeling; protein engineering; drug design; expert systems; general structure-property relationships; molecular dynamics; chemical database development and usage.

Journal of General Physiology
The mission of the Journal of General Physiology is to publish articles that elucidate important biological, chemical, or physical mechanisms of broad physiological significance.

Journal of Irreproducible Results
JIR articles should be humorous. Appeal to scientists, doctors, and engineers.

Journal of Medicinal Chemistry
The Journal of Medicinal Chemistry publishes original research on the correlation of molecular structure to biological activity with a focus on the relationships of chemistry to biological activity. This includes design and synthesis of novel biologically active compounds, molecular modifications designed to target drugs to specific tissues, the role of metabolism in drug actions, application of NMR and X-ray crystallography to investigate molecular recognition at receptors, molecular modeling studies that furnish fresh insight into the design of novel agents, and molecular biology studies to study the interaction of ligands and receptors.

Journal of Molecular Biology
Research Areas Include: Gene structure, expression, replication, and recombination in both eukaryotic and prokaryotic organisms; Structure, function, chemistry, and in vivo modification and processing of proteins, nucleic acids, and other biologically important macromolecules; Cellular and developmental biology; Genetics, structure, and growth cycles of viruses and bacteriophages.

Journal of Molecular Graphics and Modelling
The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design.

Journal of Pharmaceutical Sciences
The area of focus shall be concepts in basic pharmaceutical science and such topics as chemical processing of pharmaceuticals, including crystallization, lyophilization, chemical stability of drugs, pharmacokinetics, biopharmaceutics, pharmacodynamics, pro-drug developments, metabolic disposition of bioactive agents, dosage form design, protein-peptide chemistry and biotechnology specifically as these relate to pharmaceutical technology, and targeted drug delivery.

Medicinal Research Reviews
Appropriate topics include, but are not limited to, the underlying pathophysiology of important diseases and disease vectors; therapeutic approaches to the treatment of various diseases; the properties of molecular targets for therapeutic agents; important new methodologies facilitating the search for therapies; genomics and proteomics; structure-activity correlations of drug series; the development of new imaging and diagnostic tools; drug metabolism; drug delivery; and chemical, pharmacological, pharmacokinetic, pharmacodynamic, and clinical characteristics of important drugs.

Molecular Pharmacology
Monthly issues present original applications of biochemistry, biophysics, genetics, and molecular biology juxtaposed with innovative pharmacologic research to elucidate basic problems in pharmacology and toxicology, including areas such as molecular mechanisms involved in drug receptor-effective coupling, xenobiotic metabolism, and antibiotic and anticancer drug action.

Nature
Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology.

Nature Reviews Drug Discovery
Commissions the leaders in the field to write reviews of the highest quality, authority and accessibility.

Pharmaceutical Research
Current emphasis of the journal includes, but is not limited to, the following areas: preformulation; drug delivery and targeting; formulation design, engineering, and processing; pharmacokinetics, pharmacodynamics, and pharmacogenomics; molecular biopharmaceutics and drug disposition; and computational biopharmaceutics.

Pharmacological Reviews
Quarterly journal. Topics covered have included biochemical and cellular pharmacology, drug metabolism and disposition, renal pharmacology, neuropharmacology, behavioral pharmacology, clinical pharmacology, and toxicology.

Physiological Reviews
Provides state of the art coverage of timely issues in the physiological and biomedical sciences.

Proceedings of the National Academy of Sciences (PNAS)
Since its establishment in 1914, it continues to publish cutting-edge research reports, commentaries, reviews, perspectives, colloquium papers, and actions of the Academy. Coverage in PNAS spans the biological, physical, and social sciences.

Proteins
The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS.

Protein Science
Representative topics include, but are not limited to, the structure of proteins and strategies of determining protein structure by chemical, biophysical, and recombinant methods; peptides; protein domains; protein folding and molecular dynamics; novel isolation procedures; enzyme action and regulation; interactions of proteins with nucleic acids, lipids, ligands, and other proteins; receptor-mediated signal transduction and other trans-membrane phenomena; the functions of proteins in replication, supramolecular assembly, immune reactions, development, and other biological processes; protein trafficking, synthesis, and sorting; and the recognition, localization and signaling of proteins.

Quantitative Structure-Activity Relationships - see QSAR & Combinatorial Science

QSAR & Combinatorial Science
International forum covering high-quality results on all aspects of computer-assisted methods and combinatorial techniques, as well as their applications in organic and inorganic chemistry, medicinal chemistry, biochemistry, drug design, and materials science.

Science
A weekly, peer-reviewed journal that publishes significant original scientific research, plus reviews and analyses of current research and science policy.

Structure
Aims to publish papers of exceptional interest in the field of structural biology.

Trends in Biochemical Sciences (TiBS)
Trends in Biochemical Sciences (TiBS) is designed to keep its readers up-to-date and well informed about recent advances in biochemistry and molecular biology. In addition to topical reviews, which provide the main focus of each issue, TiBS provides a platform for debate and hypothesis where new ideas can be discussed.

Trends in Pharmacological Sciences (TiPS)
Topics covered in the journal range from molecular to behavioural pharmacology, and from current techniques to theoretical pharmacology.

PubMed online Free!
PubMed is a service of the U.S. National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.

Miscellaneous

 

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ExPASy Life Science Directory
Formerly known as Amos' WWW links page, this is an excellent meta-list of URLs relating to life sciences with an emphasis on, but not limited to, proteomics.

Glaxo Wellcome Pharmacology Guide at Universidad Autonoma de Madrid online Free!
The Pharmacology Guide is a quick reference guide to most of the important terms and concepts of pharmacology. It is not a substitute for standard textbooks, but it will act as an aide-memoire for the student who encounters the terms in the scientific literature or in exam revision. It will also help pharmacologists just starting a career in research.

The Interactive Fly at Indiana University online Free!
A cyberspace guide to Drosophila development and metazoan evolution.

Introduction to semiconductor physics
Oops, I did it again.

Medicinal Chemistry Links
Meta-list of medicinal chemistry links from the Virginia Commonwealth University School of Pharmacy.

The Signaling Gateway at Alliance for Cellular Signaling online Free!
A comprehensive and up-to-the-minute resource for anyone interested in signal transduction. This Gateway represents a unique collaboration between academia and scientific publishing and is designed to facilitate navigation of the complex world of research into cellular signaling.

Theory and Practice of Receptor Characterization and Drug Analysis at Universidad Autonoma de Madrid online Free!
Online text of a course to provide the foundation necessary for understanding receptor-ligand (receptor-drug) interactions, and the fundamentals of the techniques commonly employed for such analysis.

Modelling Software

 

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Modelling Software Meta Lists

NetSci's Lists Of Computational Chemistry Software
An excellent, well-maintained, fairly comprehensive list of computational chemistry software at NetSci.org.

Structural Biology Software Database at The Beckman Institute of UIUC Free!
This database contains programs which are thought to be of interest to researchers in the fields of structural biology, quantum chemistry, and bioinformatics.

Quantum Chemistry Program Exchange (QCPE)
QCPE promotes the practice of computational chemistry by gathering and distributing computer software for chemistry and related fields. QCPE holds approximately 772 computational chemistry systems, programs, and routines.

Accelrys, Inc. 
Accelrys, Inc. delivers software and service solutions to pharmaceutical, biotechnology, and industrial chemical research organizations. They offer a number of computational chemistry suites and programs, including:

Accord™
The Accord™ product family provides flexible cheminformatics solutions that scale from the individual researcher to the enterprise. Includes:

  • Accord ChemExplorer® - Search through your documents and files for chemical structures and reactions; it looks, works and feels like the Windows Finder.
  • Accord Chemistry Control - An Active-X control with a rich set of chemical capabilities.
  • Accord Chemistry Java Object - The Accord Chemistry Java Object brings well-proven and trusted Accord chemistry depiction to applications built and written in Java, enabling you to build effective chemistry-enabled solutions and applications in this popular programming language rapidly and efficiently.
  • Accord SDK - The Accord SDK enables power users and developers to rapidly develop advanced chemical applications, such as Combinatorial Chemistry, Property Prediction and CD-ROM database publishing.
  • Accord Database Explorer - A retrieval and browsing front-end to the Accelrys reaction databases, providing cross-database searching, hit-set management and database access control.
  • Accord Enterprise Webkit™ - a development toolkit for creating focused web-based applications that help customers perform specific tasks within Accord Enterprise Informatics (AEI).
  • Accord for Access - A project-level relational database system for creating standalone or multi-user chemistry-enabled applications.
  • Accord for Excel - A desktop chemical spreadsheet for performing chemical calculations, filtering chemical tables, sorting by chemical similarity and much, much more.
  • Accord Grid Control - A Rapid Application Development (RAD) tool for displaying multiple structures and reactions, as well as data, in a grid format.
  • Accord HTS - A complete Oracle®-based, flexible system for managing compounds and biological data.
  • Accord Inventory - Brings together compound and plate management capabilities for seamless integration with high-throughput screening workflow - increasing throughput for discovery and reducing R&D costs.
  • Accord Structure Checker - enhances the ability of an organization to understand and unify chemical information based on a customizable set of Cheminformatics rules - created to validate and interpret the chemical structure. It can be used to ensure structures conform to specific quality standards.
  • Accord Solutions for Biologists - a complete, Oracle-based system for managing compounds and assay data.
  • Accord Solutions for Chemists - Designed for chemists, screeners, pharmacologists and scientific software developers, who need the ability to register, search, and share 2D molecular structures, reactions, and associated data across the enterprise.
  • Accord Web Viewer - enables the display of 'live' molecules and reactions in a webpage, allowing users to search compound databases, register structures, and interact with common chemical drawing packages through a web browser.
  • DS Accord Chemistry Cartridge - enhances the power of Oracle for chemical applications by adding a new chemistry data type, which allows users to build solutions that store, index and search for chemical moieties.
  • DS Accord Enterprise Core - the central component of Accord Enterprise Informatics that provides sophisticated knowledge management tools to extract information from an Oracle database.
  • DS Accord for Excel Enterprise - A multi-functional module of DS Accord Enterprise for sending test data to the DS Accord Enterprise database, as well as for querying and reporting.

Catalyst
Catalyst® is an integrated environment for database management and querying tasks. Includes:

  • DBServer CATALYST®/DBServer enables you to identify structurally diverse leads using pharmacophore hypotheses as search queries for corporate or commercial databases.
  • Compare CATALYST®/Compare provides the ability to compare and fit hypotheses onto molecules.
  • Confirm CATALYST®/Confirm is a conformation generation program that calculates coverage-based conformational models, thereby allowing the handling of molecular flexibility.
  • HipHop HipHop provides feature-based alignment of a collection of compounds without considering activity.
  • HypoGen Given only available experimental information such as 2D structures and biological activities of a set of molecules, you can use Catalyst to generate general interaction hypotheses that explain variations in activity across a set of molecules.
  • Info CATALYST®/Info builds and administers databases of flexible three dimensional (3D) structures using your corporate or project data.
  • Shape CATALYST®/SHAPE generates lead compounds by searching three-dimensional corporate databases or combinatorial libraries for shape similarity between molecules.
  • Visualizer CATALYST®/VISUALIZER provides a chemistry-aware environment for modeling, visualization, structural and 3D query editing, and manual creation of pharmacophore hypotheses.

Cerius2
Cerius2 (also known as "C2" or "C2") provides a wealth of tools for applications in life and materials science modeling and simulation. The environment has particular strengths in rational drug design and structure-based drug design. Includes:

  • ADME/Tox Package provides computational models for the prediction of absorption, distribution, metabolism, and excretion (ADME) properties derived from chemical structures.
  • C2.1DSIM generates 1D similarity strings used as a descriptor in ADME/Tox model derivation.
  • C2.3DKeys provides pharmacophore fingerprint capabilities.
  • C2.Align aligns sets of molecules for easy comparison during the study of drug candidates using automated or manual alignment methods.
  • C2.Analog Builder is used to specify combinatorial libraries and select fragments/reagents based on their diversity.
  • C2.AutoLudi builds on the functionality of C2.Ludi Receptor-based de novo design in Link Mode.
  • C2.Conformers provides conformational search algorithms and associated analysis tools.
  • C2.CSAR uses a recursive partioning methodology to derive decision trees based on qualitative information.
  • C2.DBAccess provides direct access to structural databases (Catalyst and MDL ISIS) for use in modeling experiments.
  • C2.Descriptor+ extends the range of QSAR analysis in Cerius2 by supplying a wide range of generic descriptors.
  • C2.Discover is a user interface to the widely used and well-validated Discover simulation code.
  • C2.Diversity analyzes chemical diversity to design and evaluate compound libraries and reagent sets for combinatorial chemistry.
  • C2.Dynamics applies molecular mechanics to study structure relaxation and investigate the behavior of a material over a time period.
  • C2.FFE (Force Field Editor) lets you adapt force fields from the Cerius2 database or create your own.
  • C2.FieldFit performs molecular alignment based on steric and electrostatic fields, as well as alignments on moments of inertia and electrostatic moments.
  • C2.GA provides the breakthrough technology of Genetic Algorithms to evolve a family of predictive models, which helps you develop QSAR models from receptor surface and other data, leading to faster screening of drug candidates.
  • C2.LibCompare provides multiple library selection and comparison capabilities.
  • C2.LibEngine provides extremely fast calculations for a number of descriptors; it also provides very fast relocation clustering which can be used for compound selection.
  • C2.LibProfile provides constrained diversity selection within Cerius2.
  • C2.LibSelect provides combinatorial library selection capabilities.
  • C2.LibX provides capabilities for subsetting extremely large virtual libraries into realistic size subsets.
  • C2.LigandFit provides accurate and fast flexible docking and scoring capabilities for ligands to a receptor site.
  • C2.Ludi is a de novo design program that also allows you to simulate screening before performing experiments and prioritize lead candidates before you synthesize compounds.
  • C2.MFA permits field-based 3D QSAR and visualization.
  • C2.Minimizer predicts low-energy structures using molecular mechanics calculations and the power of Cerius2's Open Force Field.
  • C2.MMFF provides specialist access to the Merck Molecular Force Field for accurately studying the structure, energetics, and dynamics of molecular systems in the life sciences.
  • C2.Mopac interfaces to the popular semi-empirical quantum code MOPAC.
  • C2.NNet uses neural nets for predicting activities or activity classes in SAR analysis or in library focused design.
  • C2.OFF (Open Force Field) provides molecular mechanics force fields to support Cerius2's property prediction modules.
  • C2.QSAR+ provides a wide range of regression and analysis technologies integrated in a "chemically aware" molecular spreadsheet.
  • C2.Receptor lets you prioritize lead candidates for drug development by investigating their interaction with a protein receptor site - represented as a 3D surface.
  • C2.SBF provides structure-based focusing capabilities with fast prioritization of databases of compounds against a given target.
  • C2.X-GEN processes X-ray diffraction data for macromolecular X-ray crystallography.
  • C2.Visualizer provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements for running Cerius2 applications
  • LigandFit/CAP is a library of ligands in 3D representation prepared from the Chemicals Available for Purchase (CAP) and CAPScreening databases.
  • Ludi/CAP enables the design tools of C2.Ludi to select commercially-available chemical fragments based on Accelrys' Chemicals Available for Purchase (CAP) and CAPScreening databases.

CMD Bioscience specializes in the use of novel proprietary computational methods to model and engineer clinically important protein-protein and protein-peptide interactions. Our "Affinity" algorithm is designed to predict protein-protein / protein-peptide binding affinities; it is fast enough for use as a scoring function and will be made freely available to the academic community.

Discovery Studio
A comprehensive suite of modeling and simulation solutions for protein modeling and computational chemistry. Includes:
  • Analysis - Analyze and visualize molecular dynamics trajectories of proteins and protein-ligand complexes; animate, graph, and tabulate results.
  • Biopolymer constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing complex macromolecular structures.
  • CHARMm - Calculate energy minimization and molecular dynamics simulations.
  • CHARMm Lite - Perform in situ ligand minimization using the CHARMm simulation engine.
  • CFF, an advanced Class II forcefield, is used to optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models.
  • Discovery Studio Visualizer Free version available!
  • LigandFit - Tool for docking ligands into a binding site of a fixed macromolecular target receptor.
  • LigandFit/CAP - A library of ligands in 3D representation prepared from the Chemicals Available for Purchase (CAP) and CAPScreening databases.
  • LigandScore - Enables objective evaluation of ligand-protein interactions with scoring functions and their individual descriptors.
  • Ludi - Used for receptor-based de novo searching of fragments ('Receptor' mode) and for building on an existing ligand scaffold ('Link' mode).
  • Ludi/CAP - A fragment library derived from the CAP database designed specifically for Ludi; this library can be used for receptor-mode de novo design using the Ludi engine and can be accessed by the Ludi engine in any of its three interfaces, Discovery Studio, Insight II, or Cerius2.
  • MODELER - automatically generates a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure.
  • Protein Families - calculate multiple sequence alignments using sequence & structure information, and perform Evolutionary Trace analysis to identify functionally important residues.
  • Protein Health - Determine the quality of protein structures using the Profiles 3D verification method and perform secondary structure classification.
  • Protein Similarity Search - Identify homologs for your protein sequences by searching over the web or against locally installed databases.

Diva
Diva gives researchers the tools needed to work with their chemical and biological data.

Insight II
Insight II is a sophisticated molecular modeling environment that provides a powerful graphical interface to best-of-breed algorithms for molecular dynamics, homology modeling, de novo design, and electrostatics. Includes:

  • Affinity provides automated docking of ligands to receptors in the SBD process.
  • Binding Site Analysis combines several tools that enable you to identify and characterize a protein's binding site, then use those characteristics to look for similar features in other proteins of known structure.
  • Biopolymer constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing complex macromolecular structures.
  • CFF, an advanced Class II forcefield, is used to optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models.
  • CHARMm combines standard minimization and dynamics capabilities with expert features including free energy perturbation (FEP), correlation analysis, and combined quantum and molecular mechanics (QM/MM) methods.
  • Decipher is a powerful and flexible program for high-level analysis of molecular structure and the results of molecular dynamics simulations.
  • Delphi calculates electrostatic potentials and solvation energies of both large and small molecules, including nucleic acids.
  • Discover incorporates a range of well validated forcefields for dynamics simulations, minimization, and conformational searches.
  • Homology builds a 3D model of a protein from its amino acid sequence and the known structure of related proteins.
  • Ludi is a powerful tool for de novo rational drug design.
  • Ludi/CAP enables the design tools of Ludi to select commercially-available chemical fragments based on Accelrys' Chemicals Available for Purchase (CAP) and CAPScreening databases.
  • MCSS characterizes an active site's ability to bind given ligand probes using energetics calculated via CHARMm.
  • MODELER automatically generates a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure.
  • NMR Refine Advance expands the refinement capabilities found in NMR Refine/DG-II to include simulated annealing and restrained molecular mechanics and dynamics (MD Schedule), refinement of NOE intensities using hybrid-matrix approaches (IRMA), direct refinement of NOE volumes (NOE-MD), an interface to back-calculating 2D NOESY crosspeak intensities (NOE Simulate), and a spreadsheet method of analyzing NMR-related structural and dynamical molecular parameters (Query).
  • NMR Refine DGII provides an entry-level option into NMR refinement software with capabilities for generating structures from NMR-derived distance and dihedral restraints.
  • NMR X-PLOR streamlines the steps in structure determination from NMR data.
  • Profiles 3D searches a structural-motif database with a new sequence, looking for compatibility; searches a sequence database with an example structure, seeking similarity; or verifies the agreement between the sequence and current model of a protein sequence/structure under study.
  • Search/Compare generates and compares the conformations of different molecules.
  • SeqFold provides an algorithm to aid the functional identification of proteins.
  • Sketcher & Converter Sketcher is used to draw molecules in 2D and automatically convert them to 3D models. Converter builds 2D structural databases into 3D structural databases.
  • ZDOCKpro contains a novel set of programs for protein-protein docking.

PipelinePilot
Pipeline Pilot streamlines the integration and analysis of vast quantities of data flooding the research informatics world. (Note: Accelrys merged with SciTegic, producer of PipelinePilot, in 2004.)

Quanta
QUANTA is the leading software environment for x-ray crystallographic model building and de novo tracing.

Accord - see Accelrys, Inc.

Advanced Chemistry Development (ACD/Labs)
Advanced Chemistry Development Inc. provides a wide set of desktop and on-line software for chemists and educators: NMR, IR, UV, Mass Spectroscopy, Drawing and Modelling, Chromatography, Naming, Physico-Chemical Properties Calculation, comprehensive databases and predictions. Offerings include:

1D NMR Expert
Formerly known as ACD/Combi NMR, ACD/1D NMR Expert is a software tool that offers high-throughput processing, verification, and quantitation of 1D NMR data.

2D NMR Expert
ACD/2D NMR Expert provides NMR spectroscopists with the ideal tool for handling large amounts of 1D and 2D NMR data.

2D NMR Predictor
Calculate 2D spectra for a variety of experiments of several correlation types in heteronuclear or homonuclear environments.

Add-ins for ISIS
includes:

Aldrich NMR Library for ACD/Labs
Verify your starting materials with this commercial library of over 15,000 chemical structure database entries with assigned 1H and 13C NMR spectra.

Automation Server
ACD/Labs enables classification of tasks to be handled in a fully automated environment using ACD/Automation Server, significantly boosting laboratory productivity and efficiency.

Boiling Point
ACD/Boiling Point allows you to predict the vapor pressure of an organic compound as a function of temperature or the boiling point temperature as a function of pressure. See also:
  • Boiling Point Batch - allows rapid and automatic calculation of accurate boiling point values and related properties.

ChemBasic
A meta-language variables and data structures that allow you to drive the software with very simple, very high-level language control.

ChemCoder SDK
A software development kit that brings the power of ACD/Labs patent pending chemical structure barcode technology to your application.

ChemFolder
Provides users with the ability to create and manage databases with thousands of chemical structures, reactions, and reports in a system that lets users compare databases, predict chemical properties, group and analyze data using advanced graphics, and much more. Includes:
  • ChemCoder - a software tool enabling users to encode and retrieve chemical structures with associated data by using 2D barcodes.

Chemical Nomenclature Service
ACD/Labs will use our powerful software to quickly and accurately name your compounds.

ChemSketch  Freeware version available!
ACD/ChemSketch is an advanced chemical drawing tool and is the accepted interface into the industry's best NMR and molecular property predictions, nomenclature, and analytical data handling software. Includes:
  • 3D Viewer - Go from a publication-quality sketch to an attractive three-dimensional structure with the click of a button!
  • ChemPalm - application for Pocket PC and Palm¨ OS-based PDAs (Personal Digital Assistants). Includes:
    • CHEMiCALC - Renowned chemical calculator for ACD/ChemPalm users.
  • ChemPocket - application for Pocket PC and Palm¨ OS-based PDAs (Personal Digital Assistants).
  • Tautomers will check and generate the most common tautomeric forms of drawn organic structures.

ChromGenius
Uses a knowledge base of structures and retention times for known compounds as a basis to predict retention times and chromatograms for new compounds based on chemical structure. Includes:

CNMR Predictor
Quickly and accurately predict 13C NMR spectra, chemical shifts, and coupling constants for almost any organic chemical structure. Includes:
  • CNMR DB - contains a user-accessible internal database of 2,160,000 experimental chemical shifts and 88,400 coupling constants for over 175,000 structures.

Dictionary
A software module of ACD/ChemSketch that finds chemical structures according to their chemical, systematic, or alternative (trivial) name.

Extension for ChemDraw
A program created to integrate ACD/Labs algorithms with the CambridgeSoft ChemDrawTM interface.

FNMR
An NMR prediction software package that quickly and accurately calculates 19F chemical shifts and coupling constants for chemical structures containing fluorine.

GC Simulator
Models a hypothetical gas chromatogram for your compounds under the specified conditions on the basis of their calculated boiling points.

HNMR Predictor
Quickly and accurately predict 1H NMR spectra, chemical shifts, and coupling constants for almost any organic chemical structure. Includes:
  • HNMR DB - contains a user-accessible internal database of over 1,440,000 experimental chemical shifts and 494,000 coupling constants for over 175,000 structures.

I-Lab Intranet Edition
An innovative and cutting-edge server platform for enabling prediction and search technology.

LC Simulator
A program that predicts analyte pKa values and retention times for Liquid Chromatography separation of organic chemical mixtures under specified conditions.

LogD
ACD/LogD Suite includes, in addition to the unique tool for calculation of logD, ACD/LogD, the fully-featured ACD/pKa DB and ACD/LogP DB programs for calculating individual ionization constants and partition coefficients of neutral species. Also included is ACD/Sigma, which allows you to obtain electronic substituent constants. Also includes:
  • LogD Batch - contains the same capabilities as ACD/LogD Suite, but is stream-lined for power users who require thousands of logD values at a time.
  • LogD Sol Suite - enables batch calculation of solubility in water, including the pH-dependent solubility, intrinsic solubility and solubility in pure water.

LogP DB
Obtain accurate octanol-water partition coefficients (logP), and review an extensive library of experimental logP data. Includes:
  • LogP Accuracy Extender - calculates new increments for the ACD/LogP and ACD/Solubility algorithm.
  • LogP Batch - allows rapid and automatic calculation of accurate logP (octanol-water partition coefficients) - in most cases to ±0.3 or better - for large sets of compounds presented in an SDfile or ISIS Database format.

Method Development Suite
Combines processing and prediction tools with knowledge-based databasing capability.

Mol2Gif
A conversion utility to manage their molfile-based chemical structures in graphic interchange format (GIF)

MolX
A molecular structure editor that can be easily embedded into custom applications written in a variety of programming environments supporting ActiveX technology: C++, Delphi, Basic, or Web-related.

MS Fragmenter
Automates the rule-based task of determining the possible fragmentation of organic molecules, and displays the results for review in a convenient interface.

MS Manager Suite
Combines ACD/MS Manger, ACD/ChromManager, and ACD/UV-IR Manager to give you the functionality you need to fully process and interpret DAD, chromatographic, and MS data.

Name
A current industry standard used by numerous individuals and corporations within chemical and pharmaceutical industries to quickly and accurately name their compounds for reports, databases, patents, and publications. Includes:

Name Chemist Version
The indispensable chemist's software tool designed to help chemists generate IUPAC nomenclature, speed up literature search, and produce quality publications and reports.

NNMR
Quickly and accurately predict 15N NMR chemical shifts and coupling constants for almost any organic chemical structure.

NuGenesis Integration
This client/server technology-based software for integration with the Waters NuGenesis® Scientific Data Management System (SDMS) Platform enables connectivity to raw and processed data, and makes viewing documents and images a simple task.

Online Updater
ACD/Online Updater is a new program from ACD/Labs that allows users to check for software updates; and update all ACD/Labs software programs on their system simultaneously.

PhysChem Batch
Fast and accurate prediction of pKa, logP, logD, pH-dependent solubility, Koc, BCF, PSA, FRB, boiling point, vapor pressure, enthalpy of vaporization, flash point, and other properties. Includes:
  • ACD/pKa Batch - a program that allows rapid and automatic calculation of acid-base ionization constants (pKa values) for large sets of compounds at once.
  • ACD/LogP Batch - a program that allows rapid and automatic calculation of accurate logP (octanol-water partition coefficients) - in most cases to ±0.3 or better - for large sets of compounds presented in an SDfile or ISIS Database format.
  • ACD/LogD Batch - rapid and automatic calculation of accurate octanol-water partition coefficients for thousands of partially dissociated compounds at any pH from 0 to 14.
  • ACD/LogD Sol Batch - in addition to the above-mentioned capabilities, also enables batch calculation of solubility in water, including the pH-dependent solubility, intrinsic solubility and solubility in pure water.
  • ACD/Solubility Batch - calculates aqueous solubility for large sets of compounds presented in a number of electronic formats.
  • ACD/Sigma Batch - allows you to directly access the Hammett electronic substituent constant, s, calculated for selected fragments of your molecule or the substituents of your library for large sets of compounds presented in a number of electronic formats.
  • ACD/Boiling Point Batch - allows rapid and automatic calculation of accurate boiling point values and related properties.
  • ACD/ChemSketch Properties Batch - calculates macroscopic properties of molecules: chemical formula, molecular weight, percentage composition, molar refractivity, refractive index, molar volume, density, and the parachor, to name a few, for large sets of compounds presented in an MDL SDfile, SMILES Text File, ACD/ChemFolder Database, or MDL ISIS Database file.

pKa DB
Accurately predict the acid-base ionization constant for a wide range of organic compounds. Includes pKa Batch

PNMR
Provides users with the ability to estimate 31P chemical shifts and coupling constants for phosphorus containing compounds

Predictors for Intranets
Deploy NMR or PhysChem predictions, nomenclature services, or structure-enabled databases to numerous users throughout your corporation

Sigma
Allows you to directly access the electronic substituent constant, s, calculated for selected fragments of your molecule or the substituents of your library. Includes:
  • Sigma Batch - allows you to directly access the Hammett electronic substituent constant, s, calculated for selected fragments of your molecule or the substituents of your library for large sets of compounds presented in a number of electronic formats.

Solubility DB
Accurate prediction of aqueous solubility. Includes:
  • Solubility Batch - calculates aqueous solubility for large sets of compounds presented in a number of electronic formats.

SpecManager
Encompasses a number of technique-specific modules for analytical data processing, and also contains a report editor and a databasing component for storage and retrieval of disparate forms of analytical information. Includes:
  • 1D NMR Manager - a vendor-neutral NMR processing and databasing platform designed to provide a convenient path to effectively interpret data, make astute decisions, and communicate results both internally and externally. Includes:
    • 1D NMR Processor - Automate tedious processing and analysis tasks and ease the interpretation of NMR data through advanced multiplet analysis, verification, and quantitation techniques.
    • Aldrich Add-on Database
    • Polymer Database - commercial library of over 430 assigned polymer 1H and 13C NMR spectra.

  • 2D NMR Manager - interpretation and databasing of 2D NMR data through a simple to use interface that brings an array of 2D processing and databasing capabilities to the desktop. Includes:
    • 2D NMR Processor - Automate tedious processing and analysis tasks and ease the interpretation of 2D NMR data with advanced processing, analysis, and assignment tools.

  • ChromManager - advanced chromatographic software designed to process, database, and manage chromatographic separations such as HPLC, GC, and CE. Includes:
    • ChirBase™ Chiral Applications Databases - ChirBase, ChirBase/GC, and ChirBase/CE for ACD/Labs are chiral applications databases which allow chromatographers to locate separation methods for similar compounds that have been studied before.
    • ChromProcessor - enables convenient import, processing, and reporting of chromatography data, including PDA data, from various vendors in one interface.
    • Chromatography Applications Database - contains complete information on various separations, including the experimental results
    • Column Selector - a freeware column selection tool for Palm® OS-based PDAs and Microsoft® Windows.

  • Curve Manager - a generic instrumental analysis tool that boasts potential applications for the analysis of curves from thermal analysis (DSC, DTA, TGA), DMA, calorimetry, potentiometry (titrimetry), Voltammetry, Polarography, X-Ray Methods (Powder diffraction, Fluorescence, Photoelectron), ESR spectroscopy, kinetics, and more. Includes:
    • Curve Processor - a generic instrumental and plot analysis tool that boasts potential applications for thermal analysis (DSC, DTA, TGA, DMA), calorimetry, potentiometric titrimetry, voltammetry, polarography, x-ray (powder diffraction, fluorescence, photoelectron), and ESR, as well as kinetics, physisorption, chemisorption, porosimetry, and more.

  • MS Manager - software designed to conveniently process, interpret MS data, and easily communicate results. See also:
    • MS Processor - software designed for convenient analysis, interpretation, and reporting of mass spectral data.
    • IntelliXtract - software for automatic component determination, and molecular ion identification in LC/MS datasets.
  • UV-IR Manager - composed of three tightly integrated industry-leading modules for universal analytical data processing, for storing chemical data in a database, and for chemical drawing and reporting. See also:
    • UV-IR Processor - software for electronic, vibrational, or rotational transition spectroscopy processing, interpretation.
    • MM Spectra™ Integration - synergistic interaction of Measurement Microsystems' MM Spectra and ACD/UV-IR Manager software.
    • NIST IR Database - contains gas-phase FT-IR absorption spectra for over 5200 organic compounds compiled by both the National Institute of Standards and Technology (NIST) and the Environmental Protection Agency (EPA).
    • FDM IR Databases - Advanced Chemistry Development and Fiveash Data Management (FDM) Inc. are proud to present a product of their collaboration. The FDM FT-IR spectral collections were converted to five add-on databases in the ACD/SpecManager format including chemical structures.
    • FDM Raman Databases - The FDM Raman spectral collections were converted to two add-on databases in the ACD/SpecManager format including chemical structures.
    • Elsevier FTR & FT-IR DB - This database includes pairs of IR and Raman spectra of 500 polymers and related materials provided with drawn structures, substance/sample information collected in searchable User Data fields and Tables of Peaks.
    • S.T. Japan FT-IR Databases - This collection contains over 80,000 high-quality infrared and Raman spectra divided into up to 60 separate databases covering organic and inorganic compounds, polymers, surfactants, dyes, biochemicals, pesticides, forensics, and industrial chemicals.
    • S.T. Japan Raman Databases - The Raman database is composed of 4000 spectra measured by the National Japanese Laboratory or obtained from the S.T. Japan ICHEM library.
    • Coblentz Society Infrared DB - The Coblentz Society Special Collection of over 9000 IR spectra were digitized by NIST and are being converted to the ACD/UV-IR Manager database format allowing spectral or chemical structure searches, as well as providing capabilities to process, analyze, and interpret the vibrational patterns found in the hit.

SpecManager Enterprise
ACD/SpecManager Enterprise, based on an OracleTM latform, features an analytical database at the core of the solution, which can be directly integrated with all the spectroscopy data types of the ACD/SpecManager portfolio to unify spectroscopic, chromatographic, and other analytical curve data in a single vision.

SpecViewer
Allows you to view analytical data from multiple techniques NMR*, MS, UV, Visible, IR, NIR and Raman spectra. Note: The SpecViewer freeware is no longer offered.

SpecX
An analytical component that can be easily embedded into custom applications written in a variety of programming environments supporting ActiveX technology: C++, Delphi, Basic, or Web-related.

Structure Design Suite
Uses the accumulated knowledge of prior successful optimizations, structure-property relationship models, and accurate property foresight to help you choose your next synthetic pathway.

Structure Designer
This software affords medicinal and synthetic chemists the capability to quickly identify structural modifications to their lead compounds that will provide analogs with improved selected ADME and biological or environmental properties, yet still retain the parent compound's active core or the identified pharmacophore.

Structure Elucidator
a software tool that helps elucidation experts determine the chemical structure of small molecular unknowns using experimental spectral data.

Waters Advanced Structures Package
This Package significantly extends the capability of Waters' products.

Web Librarian
Offers viewing of ACD/ChemFolder, ACD/SpecManager, or ACD/SpecManager Enterprise databases through a Web client browser interface.

Web Librarian Web Services
ACD/Web Librarian Web Services provides a platform-independent XML (eXtensible Markup Language) Web Service using SOAP (Simple Object Access Protocol) over HTTP (HyperText Transfer Protocol) running under Microsoft Internet Information Services (IIS).

Workflow Manager
Design custom workflows and integrate with databasing applications to manage analytical data and samples.

AMBER (Assisted Model Building with Energy Refinement) at The Scripps Research Institute
"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

AutoDock at The Scripps Research Institute
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

Babel
Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0.

BioSolveIT 
BioSolveIT is a Bio- and Cheminformatics company. Our core businesses are software, services, and research collaborations. With three founders in academia, BioSolveIT has its backbone in research and catalyzes the genesis of products off basic research successes. The company is a spin-off of the world wide respected Bioinformatics research group at GMD - 'German National Research Center for Information Technology'. Offerings include:

CoLibri
CoLibri is a unique software tool for generating virtual screening libraries.

FlexS
FlexS is a computer program for predicting ligand superpositions.

FlexX 
FlexX is an extremely fast, robust, and highly configurable (FlexX-able) computer program for predicting protein-ligand interactions.

FlexV
FlexV is a free, fast, general-purpose visualiser for Unix and Linux workstations.

FTrees
FTrees is a highly efficient software tool for fuzzy similarity searching facilitating virtual HTS.

CACTVS
CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type.

CambridgeSoft 
CambridgeSoft offers computational, database, communication and drawing software for chemist, including:

ChemOffice
ChemOffice is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX for chemists, BioOffice, BioAssay, BioViz, and BioDraw for biologists, and Inventory, E-Notebook and The Merck Index for scientists. ChemOffice and BioOffice are available for Microsoft Windows.

ChemDraw
ChemDraw includes Struct?Name, ChemDraw/Excel and ChemNMR. Create stereochemically correct structures from chemical names, and get accurate IUPAC names for structures. Estimate NMR spectra from a ChemDraw structure with direct atom to spectral correlation. The ChemDraw ActiveX/Plugin adds chemical intelligence to your browser for querying databases and displaying information.

Catalyst - see Accelrys, Inc.

Cambridge Crystallographic Data Centre (CCDC) 
The Cambridge Crystallographic Data Centre (CCDC) builds, maintains and distributes the Cambridge Structural Database, a searchable database of organic and metallo-organic crystal structures. The CCDC also produce and distribute software products which make use of the data contained in the CSD. Offerings include:

ConQuest
ConQuest is the primary program for searching and retrieving information from the Cambridge Structural Database (CSD). ConQuest provides a full range of text/numeric database search options, in addition to more complex search functionality.

GOLD
GOLD is a program for calculating the docking modes of small molecules into protein binding sites. The product of a collaboration between the University of Sheffield, GlaxoSmithKline plc and CCDC, GOLD is very highly regarded within the molecular modelling community for its accuracy and reliability.

Mercury
Mercury offers a comprehensive range of tools for structure visualisation and the exploration of crystal packing.

Mogul
Mogul provides easy access to information on the preferred values of bond lengths, valence angles and acyclic torsion angles, using data derived from the CSD.

PreQuest
PreQuest is a database building program whose primary objective is to create high quality structural data files in a format searchable by ConQuest.

ReLiBase online Free! 
Relibase is the freely available database search, retrieval and analysis system for protein-ligand complex structures. Relibase+ is the commercial version of Relibase and has a number of additional features including the ability to generate proprietary databases that are searchable alongside the PDB.

VISTA
VISTA is an interactive analytical and statistical program.

Cerius2 - see Accelrys, Inc.

CHARMM (Chemistry at HARvard Macromolecular Mechanics)
CHARMM (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the CHARMM program.

Chem3D - see CambridgeSoft

ChemACX - see CambridgeSoft

ChemDraw - see CambridgeSoft

ChemFinder - see CambridgeSoft

ChemNMR - see CambridgeSoft

ChemOffice - see CambridgeSoft

Daylight Chemical Informatics Systems, Inc.
Daylight provides software which delivers state-of-the art chemical information processing to individual users and enterprise systems. We invented and support the SMILESTM, SMARTS, and SMIRKS chemical languages. Offerings include:

Clustering Package
The Daylight Clustering Package provides all the programs needed to cluster large sets of chemical structures and/or reactions.

Conversion Package
The Daylight Conversion Package is a set of programs which can convert molecules in MDL formats to and from Daylight formats.

DayCart
DayCart® is a fully integrated set of tools that extends Oracle clients and servers with chemical intelligence and ability.

Daylight Toolkit
The Daylight Toolkit is a programming library that provides all functions needed for chemical information processing and substructure pattern searching along with fingerprinting and similarity capabilities.

PCModels
PCModels is a Daylight software module providing access to two chemical models: CLOGP (hydrophobicity partition coefficient) and CMR (molar refractivity). These models are developed and supported by BioByte, Inc. of Claremont, CA.

Properties Package (incl. DayPropTalk, TautomerTalk, DayProp)
The Daylight Property package is designed to meet the demands of virtual screening and provides for the rapid estimation of physical properties directly from molecular structure.

THOR-Merlin Toolkit
The THOR-Merlin Toolkit is a programming library which provides a comprehensive programmatic interface to THOR and Merlin Servers.

Discovery Studio - see Accelrys, Inc.

DOCK at UCSF Free for academics!
DOCK addresses the problem of "docking" molecules to each other.

Elsevier MDL 
Elsevier MDL is the pioneering leader in discovery informatics, offering products such as:

Autonom
AutoNom 2000 (Automatic Nomenclature) is a chemical-name-generating program that assigns systematic IUPAC (International Union of Pure and Applied Chemistry) chemical names to drawn structures in seconds.

MDL Central Library
Enterprise-wide information management for parallel and combinatorial synthesis

MDL Chemscape
Chemscape Server is a communication device that allows a Web server to communicate with MDL ISIS/Host for performing registration, searching, and browsing across a variety of chemical, textual, and relational database types.

MDL Cheshire
MDL Cheshire is a chemical scripting language and an interactive prototyping environment for building, validating, and using "rules" that analyze and interpret chemistry.

MDL Chime Free version available!
Chime is a browser plug-in that renders 2D and 3D molecules directly within a Web page.

MDL Chime Pro
MDL Chime Pro for Web is a browser plug-in that renders 2D and 3D molecules directly within a Web page; MDL Chime Pro for Java is a JavaBean component that enables developers to provide chemical structure rendering and visualization in pure Java applications and Applets as well as in Web pages.

MDL Isentris
As the successor to MDL ISIS, MDL Isentris is the world's first discovery platform designed to accelerate research by providing an n-tier platform to support integrated applications, data and business rules. Includes:

  • MDL Base Delivering the power of MDL Isentris, MDL Base provides unparalleled search, view and print capabilities to access integrated scientific data in an easy-to-use and dynamic environment that supports researcher's workflow
  • MDL Core Interface is the middleware of a modern three-tier application development framework built on industry-standard technologies.
  • MDL Direct, MDL's Oracle integrated data cartridge, drives database access within the Isentris system.
  • MDL Draw Enterprise Edition A next-generation chemical drawing package

MDL ISIS
MDL ISIS (Integrated Scientific Information System) serves as an information management framework for discovery data. Includes:

  • MDL ISIS/Base is a flexible desktop database management system for storing, searching, and retrieving chemical structures and associated scientific data.
  • MDL ISIS/Draw is a chemically intelligent drawing package that enables you to draw chemical structures using the same intuitive signs and symbols used for paper sketches. Free version available!
  • MDL ISIS for Excel lets scientists retrieve and manipulate biological and chemical data and chemical structures in a Microsoft Excel spreadsheet environment.
  • MDL ISIS/Host is the server foundation for the ISIS (Integrated Scientific Information System) family of products.

MDL Reagent Selector
Reagent Selector offers scientists engaged in medium- and high-throughput synthesis integrated tools for selecting reagents, locating and obtaining compounds from in-house inventories, and "shopping" from databases of commercial suppliers.

MDL Registration
MDL Registration is a flexible, new-generation registration system for building a corporate substance and batch database.

MDL Report Manager
MDL Report Manager is an easy-to-configure reporting tool that uses MDL ISIS chemical structure searching and live structure reporting to integrate and extract data from multiple databases into pre-formatted reports.

Evolutionary Trace at Baylor College of Medicine  online Free to academics!
Ranking the relative functional importance of amino acids in a protein sequence by correlating their variations during evolution with divergences in the phylogenetic tree of that sequence family. Includes:
  • Evolutionary Trace Viewer - View Evolutionary Trace results; modify existing traces; run new traces.
  • Evolutionary Trace Report Maker - Pools from different sources information about protein sequence, structure and elementary annotation, and to that background superimposes inference about evolutionary behavior of individual residues, using real-valued evolutionary trace method.
  • Evolutionary Trace Server - The Evolutionary Trace is available for use on our server via two front-end programs that provide different means of running a trace and viewing results.

Expression Profiler at the European Bioinformatics Institute online Free! 
A set of tools for clustering, analysis and visualization of gene expression and other genomic data. Includes:

EP:PPI
Protein-Protein Interaction data analysis.

EP:GO
GeneOntology browser and analysis tool.

URLMAP
Data integration via web forms.

SPEXS
Sequence Pattern EXhaustive Search, a sequence pattern discovery tool.

PATMATCH
Sequence pattern matching and visualization.

SEQLOGO
Sequence logo drawing tool.

GENOMES
Study full genomic sequences, functional classes.

GPCR 
GPCR/G-protein coupling specificity study.

Gaussian
Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types.

Gene Map Annotator and Pathway Profile (GenMAPP) at the University of California, San Francisco online Free!
Visualize gene expression and proteomics data on pre-packaged and custom pathways (MAPPs) with criteria you design. Includes MAPPFinder 2.0, MAPPBuilder 2.0, MAPP Converter and a customizable database format to support any species or gene ID system.

GROMACS (Groningen Machine for Chemical Simulations)
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Hypercube, Inc.
Hypercube has been a leader in molecular modeling since the company was founded in 1982. Offerings include:

HyperChem
HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use.

Insight II - see Accelrys, Inc.

LHASA at Harvard University 
LHASA (Logic and Heuristics Applied To Synthetic Analysis) at Harvard is the home for LHASA synthesis design, DEREK toxicology prediction, and LCOLI combinatorial library design software. Offerings include:

Retrosynthetic Analysis
The retrosynthetic analysis module in LHASA allows you to identify novel pathways and derive complete synthetic routes from the target molecule to available starting materials.

Reaction Prediction for Combinatorial Chemistry
Transforms in the LHASA knowledge base are used in the forward direction, generating multiple products from single reactants or virtual combinatorial libraries from pools of starting materials.

DEREK
The LHASA DEREK system can deliver predictions about a broad variety of toxicological properties of your compounds.

PROTECT
Automatically find the best steps for protection and deprotection, using a wide selection of protective groups.

APSO Synthetic Chemistry Training
Designed for undergraduate organic chemistry students, APSO represents a perfect companion to the LHASA retrosynthetic analysis module. The APSO interface guides the student through the choice of reactions, displaying positive results or the reasons for reaction failure.

Lhasa Limited
Lhasa Limited is a well established not-for-profit company and educational charity located in Leeds, England. Lhasa Limited is a leading global supplier of knowledge based software and associated databases for use in metabolism, toxicology, and related sciences. Offerings include:

DEREK for Windows
Derek for Windows is a computer program that is used by toxicologists and other scientists who are interested in understanding whether a chemical is toxic in humans, other mammals and bacteria.

METEOR
Meteor is used by scientists with an interest in understanding the metabolic fate of chemicals.

VITIC
Vitic is a toxicity database that has been specially developed for researchers who need efficient access to toxicology information, even when the information resides in multiple databases in different locations.

LigandScout from Inteligand
A software tool that allows to rapidly and transparently derive 3D pharmacophores from structural data of macromolecule/ligand complexes in a fully automated and convenient way.

LIGPLOT at University College London/Inpharmatica Free for academics!
Program for automatically plotting protein-ligand interactions.

Molecular Networks GmbH 
Molecular Networks GmbH (www.mol-net.com) provides multifaceted, innovative software to the chemical, biotechnology and pharmaceutical industry. Offerings include:

2DCOOR
2DCOOR generates 2D coordinates suited for 2D depictions of publishing quality.

ADRIANA.Code
ADRIANA.Code calculates a series of molecular descriptors that can be applied in the area of in silico discovery and optimization of new chemical entities.

C@ROL
C@ROL is a chemical warehouse system designed to store 2D structures and multiple 3D conformations of chemical compounds along with experimental data.

CHECK
CHECK performs high throughput structure integrity checks and can be used to normalize the state of each compound.

CONVERT
CONVERT enables the seamless inter-conversion of 40 different structure and reaction file formats.

CORINA
CORINA generates 3-dimensional molecular models starting from atom type and connectivity information only.

CORINA-F
CORINA-F is a low cost feature-limited version of CORINA that is specifically designed to extend capabilities of the docking program FlexX developed by BioSolveIT.

FM3D
FM3D is a Unix/Linux-based desktop application for the visualization and manipulation of 3D molecular models such as those obtained by CORINA.

ROTATE
ROTATE automatically generates conformational ensembles from a starting 3D structure like the one obtained with CORINA, including conformers, which come close to biologically active ones.

SONNIA
SONNIA is a self-organizing neural network package including both unsupervised (Kohonen) and supervised (counter-propagation network) learning techniques.

STERGEN
STERGEN automatically identifies stereocenters and enumerates all possible combinations of stereoisomers.

TABLE
TABLE converts files containing structures and data into spreadsheet and internet compatible file formats.

TAUTOMER
TAUTOMER enumerates all tautomeric forms of a compound.

WODCA
WODCA provides synthesis design solutions for organic compounds.

Molecular Operating Environment (MOE)
MOE is a comprehensive software system addressing the needs of today's research disciplines including Bioinformatics, Cheminformatics, Protein Modeling, Structure-Based Design, High Throughput Discovery and Molecular Modeling and Simulations.

MolSoft LLC 
Molsoft a leading provider of tools, databases and consulting services in the area of structure prediction, structural proteomics, bioinformatics, cheminformatics, molecular visualization and animation, and rational drug design. Offerings include:

BeeHive
BeeHive is a versatile research informatics platform born out of collaboration between Molsoft and Biovitrum AB, Sweden.

ICM Browser
ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. "Pro" version also available.

ICM Pro
Easy and complete desktop-modeling environment for a biologist or a chemist interested in molecular structure and function.

ICM Virtual Ligand Screening (ICM-VLS)
ICM Virtual Ligand Screening is a combination of the genuine internal coordinate docking methodology with a sophisticated global optimization scheme.

MolCart
MolCart is a perfect addition to the ICM cheminformatics tools. It allows you to handle very large libraries of chemical compounds.

OpenEye Scientific Software
OpenEye provides software to the pharmaceutical industry for molecular modeling and cheminformatics. Central to our approach is the importance of shape and electrostatics as primary variables of molecular description, platform-independent code for high-throughput 2D and 3D modeling, and a preference for the rigorous rather than the ad hoc. Offerings include:

AFITT
Crystallographic refinement and analysis.

BROOD
Bioisostere identification using shape, chemistry and electrostatic similarity.

CASE
The Case Toolkit is an extensible programming library that provides generalized function optimization in a wide array of coordinate spaces.

EON
Chemical similarity analysis via comparison of electrostatics overlay.

FILTER
Molecular screening and selection based on physical property or functional group.

FRED
Extremely fast, systematic docking search for ligand binding within a protein active site.

LEXICHEM
Lexichem provides efficient conversion of chemical names to chemical structures and vice versa, where chemical names can be standard IUPAC names or more common traditional names.

OEChem
OEChem is a programming library for Chemistry and Chemical Informatics that is fast and has a stable, documented API.

Ogham
Ogham is designed to artfully render 2D Kekule drawings from molecular connectivity information.

OMEGA
Systematic high-throughput conformer generation, including 1D or 2D to 3D structure generation.

QUACPAC
Quality charge states and charges for small molecules and proteins.

ROCS
Chemical similarity analysis via rapid 3D molecular shape searches.

SCUT MONKEYS
A suite of Python scripts that address Some Common Unfinished Tasks (SCUT). Among others, file format conversion, passing SD tag data to Excel spreadsheets, determining RMSD between similar structures, and cleaning up structures pulled from a database.

Shape
The Shape Toolkit facilitates the incorporation of molecular overlay capabilities into other applications, for example ROCS, our 3D molecular shape comparison program.

SMACK
Molecular databases query converter and optimizer (SMARTS and MDL).

SZYBKI
Fast structure optimization of ligands in gas-phase, solution, or within a protein active site.

VIDA
Graphical user interface that visualizes, analyzes and manages corporate collections of molecular structures and information.

WABE
Electrostatics optimization of a lead compound.

Zap
The Zap Toolkit produces PB electrostatic potentials and, from them, biologically interesting properties including solvent transfer energies, binding energies, pKa shifts, solvent forces, electrostatic descriptors, surface potentials and effective dielectric constants.

OSIRIS Property Explorer online Free!
Lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid.

PipelinePilot - see Accelrys, Inc.

PreBIND at Mount Sinai Hospital (Canada)
A data mining tool to locate biomolecular interaction information in the scientific literature.

PREDKIN at U. Queensland  online
The program produces a prediction of substrates for serine/threonine protein kinases based on the primary sequence of a protein kinase catalytic domain.

PyMol Free!
A free and flexible molecular graphics and modelling package which can be also used to generate animated sequences.

Quanta - see Accelrys, Inc.

RbDe at Weill Medical College of Cornell University Free!
A web application to create and edit residue-based diagrams of (mostly transmembrane) proteins.

Schrödinger
Schrödinger provides accurate, reliable, and high performance computational technology to solve real-world problems in pharmaceutical, biotechnology, and materials science research, including:

CombiGlide
CombiGlide is a structure-based virtual screening program for the design of optimal, focused combinatorial libraries.

Epik
Epik is the program of choice for accurate enumeration of ligand protonation states in biological conditions.

Glide
Glide: A complete solution for ligand-receptor docking.

Jaguar
Jaguar is a high-performance ab initio package for both gas and solution phase simulations.

Liaison
Liaison applies linear interaction approximation to accurately compute binding affinities for series of ligands with similar binding modes, making it a powerful tool for lead optimization.

LigPrep
LigPrep: Versatile generation of accurate 3D molecular models.

MacroModel
MacroModel combines leading force fields, accurate effective solvation models, and advanced conformational searching methods to provide the most complete molecular modeling package suitable for a wide array of research.

Maestro
Maestro is the unified interface for all Schroedinger software.

Phase
Phase is a complete package of pharmacophore modeling tools that offers scientists an unparalleled level of control at each step.

Prime
Prime is a fully-integrated protein structure prediction program.

QuikProp
QikProp efficiently evaluates pharmaceutically relevant properties for over half a million compounds per hour, making it an indispensable lead generation and lead optimization tool.

QSite
QSite applies quantum mechanics to the reactive center of a protein active site and molecular mechanics to the rest of the system.

SiteMap
SiteMap provides researchers with an efficient means to find and better exploit the characteristics of ligand binding sites.

Strike
Strike (Statistical tool for revealing insight and knowledge) is a statistical modeling package designed especially for chemists.

Spotfire, Inc.
Analytic applications creating an information advantage. Offerings include:

DecisionSite
The Spotfire DecisionSite suite of products offer researchers, engineers and analysts in the life sciences, energy and manufacturing industries, as well as academic and government institutions, a direct, interactive, visual approach to data analysis that rapidly reveals insights and unexpected relationships to solve problems.

Swiss Institute of Bioinformatics
An academic not-for-profit foundation established on March 30, 1998 whose mission is to promote research, the development of databanks and computer technologies, teaching and service activities in the field of bioinformatics, in Switzerland with international collaborations. Software offerings include:

SWISS-MODEL online Free!
A fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

Swiss-Pdb Viewer (DeepView) Free!
DeepView - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

SymBioSys, Inc.
Simulated Biomolecular Systems Inc. (SimBioSys) is focused on research and software development in the area of biomolecular modelling. The company provides interactive visual computing and modeling solutions for biomolecular sciences. Offerings include:

CAESA: Computer Assisted Estimation of Synthetic Accessibility
CAESA automatically ranks sets of molecules according to their ease of synthesis and displays the synthesis route.

CLiDE (Chemical Literature Data Extraction)
CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature.

eHiTS (Electronic High Throughput Screening)
For fast, flexible docking of whole or partial structures to target receptors.

SPROUT
The SPROUT product line is comprised of three products:
  • SPROUT Classic is a de-novo ligand design software system.
  • SynSPROUT is a de-novo ligand design software system which uses synthetic rules to join fragments.
  • SPROUT-LeadOpt is specifically designed to aid in the lead optimization process of drug discovery.

The Theoretical and Computational Biophysics Group (TCBG) at the Beckman Institute of UIUC
The TCBG brings the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. Offerings include:

BioCore Collaboratory Environment
A collaborative work environment for biomedical research, research management and training. In addition to accessing the BioCoRE server that we are running at the Theoretical and Computational Biophysics Group via the internet, you can install your own server software.

MD Service Suite
A collection of programs, scripts, and utilities we provide for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets. Includes:

  • JMV: Java Molecular Viewer - JMV is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use platform neutral molecular visualization tool, which can be used standalone or integrated into other programs.
  • CatDCD - Concatenates DCD multiple trajectory files, can select subset of atoms, think of Unix "cat".
  • Chemical2vmd - Lets VMD act as a helper application for chemical/x-vmd MIME type in web browsers
  • Conect2psf - Converts PDB "CONECT" records into a "PSF" file for proper bond display in VMD.
  • FlipDCD/FixDCD - DCD trajectory file endianism and header conversion.
  • MDAPI - Application programming interface for molecular dynamics simulation engines.
  • MDEnergy - Calculate energies from DCD or PDB files.
  • MD Service Suite for Python - Protein structure and dynamics analysis classes.
  • MDX - Collection of C libraries to enable development of methods for molecular dynamics of biomolecules.
  • MatDCD - A Matlab package for reading and writing DCD format trajectory files.
  • Mindy - A "minimal" molecular dynamics program based on the NAMD source code.
  • Mol_Volume - A program for calculating macromolecular volume.
  • PDBCat - A tool for PDB file text processing and conversion.
  • SODIUM - Arrange ions around biological macromolecules.
  • Wat2ions - Places ions in a water bath. A companion program to Delphi.

NAMD Free!
A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet.

VMD Free!
A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

TINKER at Washington University in St. Louis Free!
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field.

Tripos, Inc.
Tripos focuses on integrating leading-edge technology and innovative science to deliver consistently superior research products and services for the biotechnology, pharmaceutical, and other life science enterprises. Offerings include:

Advanced Computation
This SYBYL module delivers the industry's fastest and most flexible systematic conformational searching algorithm.

Almond
Almond offers a new generation of molecular descriptors and a statistical workbench with which to rapidly create and test structure-activity relationship hypotheses.

AMPAC
AMPAC is recognized by researchers worldwide as a fast and robust semiempirical modeling package, with a wide variety of computational methods and an extensive set of tools to aid in the study of both molecular structure and chemical reactions.

Auspyx Data Cartridge
The Auspyx data cartridge does the supporting work required to store chemical structure information in Oracle.

Benchware
Benchware is a unique suite of laboratory informatics software specifically designed to meet the challenging demands placed on today's laboratory chemists. Includes:

  • Benchware 3D Explorer provides the means for any life science researcher to make more informed decisions by employing 3D molecular visualization on their desktop PC.
  • Benchware Discovery 360 is a ground-breaking Integrated Discovery Environment that provides scientists and research managers with a single point of entry from which they can access, analyze & share data from disparate repositories of biological and chemical data.
  • Benchware Dock enables laboratory chemists to rapidly test compound ideas, prior to synthesis, against 3D models of target protein structures, using docking calculations previously defined by molecular modeling specialists.
  • Benchware HTS DataMiner offers functionality dedicated to the location, definition and prioritization of prospective lead series from screening data sets of any size. Benchware HTS DataMiner was formerly marketed by Tripos under the product name SARNavigator.
  • Benchware LibraryDesigner is a unique program which was developed to assist the laboratory chemist decide which reactants to use, usually from a very long list of potential reactants.
  • Benchware LibraryMaker is an intuitive, Windows-based application for enumerating both small parallel libraries as well as very large virtual combinatorial libraries.
  • Benchware Notebook provides an open, service-oriented architecture that is designed to cost-effectively integrate with existing enterprise systems, including Laboratory Information Management Systems (LIMS), compound registration and inventory tracking systems.

Biopolymer
Biopolymer provides the tools needed for building and manipulating peptide, protein, DNA/RNA, and carbohydrate structures.

ClogP/CMR
The ClogP/CMR application provides highly accurate calculated logP and MR values. These methods were originally developed during the Pomona College Medicinal Chemistry Project, as part of over two decades of research by Dr. Corwin Hansch and Dr. Albert Leo (now of BioByte Corporation).

CombiLibMaker
CombiLibMaker creates virtual libraries and works with DiverseSolutions or Selector for the design of diverse or focused libraries.

Composer
Composer automatically constructs protein models using knowledge-based homology modeling methods.

Concord
Concord sets the industry standard for extremely rapid conversion of 2D (or crude 3D) input to accurate, geometry-optimized 3D structures.

Confort
Confort is a powerful conformational analysis tool that performs exhaustive yet rapid analysis of drug-sized molecules. It can be used to identify the global minimum energy conformer, all local minima within a user-specified energy range, or a maximally diverse subset of conformers.

CScore
CScore uses multiple types of scoring functions to rank the affinity of ligands bound to the active site of a receptor.

DISCOtech
Starting from a set of precomputed conformers for a set of ligands, DISCOtech uses clique detection1 methods to generate multiple pharmacophore hypotheses that can be compared and refined.

Distill
Distill is a hierarchical clustering tool that classifies compounds according to their common substructures and organizes the results in a display that enables visualization of SARs.

DiverseSolutions
DiverseSolutions is a suite of chemically intuitive tools for addressing a variety of diversity-related tasks, including: compound acquisition, iterative lead follow-up, focused and diverse library design, de novo design, and visualization of compounds and entire libraries in chemistry-space.

Dynamics
Dynamics provides a number of techniques for producing ensembles, as well as the graphical tools required for organizing and analyzing the resulting structures.

EA Inventor
EA-Inventor is a new and different approach to de novo design. It enables researchers to "invent" new compounds (for in silico lead discovery), new R-groups around a fixed scaffold (for lead exploration), or new scaffolds (for lead- or scaffold-"hopping").

FUGUE
FUGUE is an application for recognizing distant structural homologs of a target sequence by sequence-structure comparison.

GALAHAD
GALAHAD aligns a set of molecules that share a common mode of biological activity, and develops a corresponding pharmacophore hypothesis.

GASP
GASP performs pharmacophore elucidation without requiring prior knowledge of pharmacophore elements or constraints. Using a genetic algorithm, GASP automatically allows conformational flexibility and maps features among molecules.

GeneFold
GeneFold identifies a protein's function from its amino acid sequence.

GSSI
GSSI is a novel, general approach to modeling solution-phase properties through a fairly rigorous yet efficient consideration of solute-solvent interactions.

hint!
hint! provides tools to visualize and calculate the relative strengths of non-covalent interactions between and within biological molecules.

HiVol
HiVol enables the analysis and exploration of the large data sets typical of high-throughput synthesis and screening efforts.

HCSF
HSCF is a unique semi-empirical molecular orbital (MO) "information server."

HQSAR
Hologram QSAR (HQSAR) uses molecular holograms and PLS to generate fragment-based structure-activity relationships.

LeapFrog
LeapFrog is a powerful de novo ligand design tool that proposes a series of new, potentially active ligand molecules, even when the receptor structure is not known.

Legion
Legion creates virtual combinatorial libraries that can be used to design diverse or focused libraries for screening or lead optimization.

Matchmaker
MatchMaker uses an inverse-folding method to predict the 3D structure of a protein from its amino acid sequence.

MM4
MM4 is the latest in the well-known series of molecular mechanics programs developed by Prof. N. L. Allinger and co-workers at the University of Georgia. (See also MM3.)

MOLCAD
Advanced visualization of molecular surfaces and properties

Molconn-Z
Molconn-Z calculates structural descriptors for use with statistical methods in order to create QSAR and QSPR models that predict biological activity or physical properties of new molecules.

OptDesign
OptDesign is a tool to design combinatorial libraries that address the practical constraints of library synthesis.

ProTable
ProTable uses the SYBYL Molecular Spreadsheet to analyze and evaluate protein structures.

QSAR with CoMFA
QSAR with CoMFA builds statistical and graphical models that relate the properties of molecules (including biological activity) to their structures.

Protoplex
ProtoPlex allows users to control the protonation, deprotonation, or tautomerization for each chemical class of proto-centers, as well as the overall rules for formal charge and number of proto-centers to multiplex.

RACHEL
Starting from a ligand/receptor structure, RACHEL performs automated combinatorial optimization of lead compounds by systematically derivatizing user-defined sites on the ligand.

SAVOL
Calculate molecular surface and volume properties.

Selector
Selector characterizes, compares, and samples sets of compounds.

SiteID
SiteID provides analysis and visualization tools leading to the identification of potential binding sites within or at the surface of biological targets.

Stereoplex
StereoPlex generates multiple stereoisomers of each input structure according to a user-specified limit on the number of stereoisomers and a user-specified priority rule which tells the program which stereoisomers to generate if the complete set would exceed the user's limit.

Surflex-Dock
Ligand-receptor docking and virtual screening.

Sybyl
SYBYL is a suite of computational informatics software designed to enhance the drug discovery workflows and decision-making of today's computational chemists and molecular modelers.

Tuplets
Tuplets enables researchers to retrieve compounds from molecular structure databases that are pharmacophorically, and therefore biologically, similar to known actives without the need to derive a classical 3D pharmacophore model.

UNITY
UNITY combines database searching with the molecular design and analysis tools in SYBYL to provide an integrated environment for new compound discovery.

VolSurf
VolSurf reads or computes 3D molecular interaction fields and uses image processing methods to convert these fields into simple molecular descriptors that are easy to understand and interpret.

Viseur - see entry under "Target Areas->GPCRs"

Wavefunction, Inc. 
Wavefunction is dedicated to providing easy-to-learn and easy-to-use molecular modeling tools for chemistry researchers and educators. Offerings include:

Spartan
With unsurpassed visualization and a wide range of well documented computational methods in a single user-friendly software tool, Spartan delivers the full power of molecular modeling to chemists everywhere.

Trident
A new suite of molecular modeling software developed for chemists working in drug design. Trident provides medicinal chemists with access to easy-to-use molecular modeling tools.

YAeHMOP
YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.

Patents

 

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Chemical Abstracts Service (CAS) see entry under "Literature"

esp@cenet online Free!
More than 50 million patent documents from around the world, most of which are patent applications, not granted patents; patent families, telling you if very similar patents have been claimed in other countries; legal status information; and bibliographic data of non-patent literature ("XP" documents).

Patent Application Information Retrieval (PAIR) at the United States Patent Office  online Free!
Offers the public an advanced electronic portal to PDF viewing, downloading and printing an array of information and documents for approximately 500,000 patent applications not covered by confidentiality laws.

PatentScope online Free!
This facility allows you to search 1,155,607 international patent applications and to view the latest information and documents available to the International Bureau.

United States Patent and Trademark Office (USPTO) online Free! 
Our website provides full text for patents issued from 1976 to the present. We provide TIFF images for all patents from 1790 (YES, REALLY 1790) to the present.

Target Areas

 

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  • Meta Lists

    Molecular Class-Specific Information System (MCSIS) at Radboud University et al.
    A relational database-centered system to aid researchers with the collection and dissemination of data. Includes subsections on:
    GPCRDB
    An information system for G protein-coupled receptors. See entry under "Target Areas->GPCRs"

    GPCRIPDB
    An information system for GPCR interacting proteins.

    NucleaRDB 
    An information system for nuclear receptors.

    Nuclear Receptor Mutation Database 
    A database for nuclear receptor mutation information. It includes mutation information from SWISS-PROT/TrEMBL, several web-based mutation data resources, and data extracted from the literature in a fully automatic manner.

    PrionDB
    A molecular specific information system for prion proteins.

    KChannelDB
    A molecular specific information system for potassium channels.

    Protein Families at proweb.org
    A list of links to web sites about various protein families.

  • GPCRs - G-Protein Coupled Receptors

    G protein-coupled receptor definition at Wikipedia

    7TMR List at ExPASy
    List of 7-transmembrane G-linked receptor entries.

    Endogenous GPCR List at tumor-gene.org
    A list of the endogenous GPCRs expressed in various cell lines.

    GLIDA - GPCR-Ligand Database at Kyoto University online Free! 
    A novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands.

    GPCR Coupling Specificity Website - see entry under "Modelling->Modelling Software->Expression Profiler"

    GPCRDB: Information system for G protein-coupled receptors (GPCRs) online Free! 
    The GPCRDB WWW hypertext document represents the beginning of a fully integrated GPCR information system. This system will in due time combine data, browsing tools and query tools. The main topic of this document is the superfamily of seven transmembrane helix containing G protein receptors, or for short GPCRs. However, also GPCR related information such as G protein sequences will be stored.

    GPCR fingerPRINTS
    PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite.

    GPCR Pattern Recognition at University College London online Free!
    A diagnostic resource for 7TM proteins. You may search a query sequence against the fingerprint database to determine if it belongs to one of the characterised superfamilies, families or receptor subtypes (~120 fingerprints are now available).

    GRIFFIN G-Protein-Receptor Interacting Feature Finding INstrument at the Computational Biology Research Center (Japan) online Free! 
    A high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight.

    IUPHAR Receptor Database at The International Union of Pharmacology online Free!
    The database now contains detailed information on 166 G Protein-Coupled Receptors (GPCRs) classified into 58 receptor families. Includes:

    • GPCR Database - a database of GPCR information.
    • 7TM Receptor List - a catalogue giving IUPHAR-approved nomenclature (where available), known ligands and gene names for all of these potential receptors (excluding sensory receptors and pseudogenes) together with links to curated sequence and descriptive information in the LocusLink database.

    Olfactory Receptor DataBase (ORDB) at Yale University online 
    ORDB began as a database of vertebrate olfactory receptor genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. See also:

    Predicted Ligands and Coupled G Proteins at the National Institute for Medical Research (UK) online Free!
    A listing of GPCR classifications by phylogenetic-tree based hidden Markov models.

    Viseur at Cornell University Free! 
    Viseur is a program that let you manage and visualize your preferred GPCRs (G Protein-Coupled Receptors). This program runs on SGI machines (IRIX 5.3, 6.1, 6.2, 6.3, 6.4).

  • Ion Channels

    Ion Channel definition at Wikipedia

    Ion Channel Web Links
    A meta-list of ion channel links on the web.

    IUPHAR Ion Channel Compendium at the International Union of Pharmacology  online
    The second edition of this comprehensive volume is now available online from Pharmacological Reviews. Edited for IUPHAR by William Catterall and George Gutman, this expanded and updated volume covers the molecular, biophysical and pharmacological properties of the voltage-gated ion channels that are encoded by the human genome.

    Ligand-Gated Ion Channel Database at the European Bioinformatics Institute  online Free!
    In the LGIC Database you will find the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.

  • Kinases

    Kinase definition at Wikipedia

    Kinase.com from Sugen, Inc. and the Salk Institute.
    Explores the the functions, evolution and diversity of protein kinases through analysis of kinomes - the full complement of protein kinases of any sequenced organism. It includes our extensive KinBase database, and papers and supporting material for our published work from Sugen and the Salk Institute.

    Kinase3D at Gen2X LLC
    The largest database of protein kinase 3D homology models. Sequences published and accessible @ Kinase.com were used to create over 1200 models of protein kinases from humans and model organisms. Freely accessible to academic users upon request.

    Kinases in Genomes (KinG) at the Indian Institute of Science
    A comprehensive collection of Ser/Thr/Tyr specific protein kinases and similar sequences encoded in the completed genomes of eukaryotes and prokaryotes.

    KinBase at Sugen, Inc.  online Free! 
    KinBase holds information on over 2000 protein kinase genes found in the genomes of human, mouse, fruit fly, nematode worm, slime mold and yeast. You may search the database by a variety of different gene names and accessions, or according to the sequence based classification.

    Phospho.ELM (formerly PhosphoBase) at EMBL  online Free! 
    The Phospho.ELM database contains a collection of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins. The entries, manually annotated and based on scientific literature, provide information about the phosphorylated proteins and the exact position of known phosphorylated instances.

    The Protein Kinase Resource at UCSD and SDSC  online Free!
    An effort to integrate all facets of protein kinase information and make it available online. Goals of the PKR are to provide transparent information retrieval, comprehensive data integration, instructional resources, search, analysis and visualization tools.

    Scansite at MIT  online Free!
    Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

  • Nuclear Receptors

    Nuclear Receptor definition at Wikipedia

    Mutation Database at Retina International
    Mutations of the photoreceptor cell-specific nuclear receptor (NR2E3, PNR).

    Nuclear Receptor Database (formerly at UCSF) - see entry for NucleaRDB under "Target Areas->Meta Lists"

    Nuclear Receptor Database (NuReBaSe) at ENS-Lyon online Free!
    A reference database on Nuclear Hormone Receptors.

    Nuclear Receptor Mutation Database - see entry "Target Areas->Meta Lists"

    Nuclear Receptor Resource (NRR) at Georgetown University online Free!
    A collection of individual databases on members of the steroid and thyroid hormone receptor superfamily, each forming a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. Includes:

    Nuclear Receptor Signaling Atlas (NURSA) at the Baylor College of Medicine online Free!
    The primary directive of the NURSA program is to gather and organize information relating to key aspects of orphan nuclear receptor biology, with the aim of extending this blueprint to the wider discipline of nuclear receptor signaling.

    Nuclear Receptors: The Ultimate Resource at the University of Nijmegen (Holland)
    Paolo Guarnieri's nuclear receptor links from 2002.

Textbook Publishers

 

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CRC Press
Publishes books, journals, and electronic materials in biology, medicine, environmental science, engineering, business, mathematics, statistics, etc. Subject areas include:

Elsevier Books
Elsevier is an integral partner with the scientific, technical and health communities, delivering superior information products and services that foster communication, build insights, and enable individual and collective advancement in scientific research and health care. Subject areas include:

John Wiley and Sons, Inc. 
A leading publisher for the scientific, technical, and medical (STM) communities worldwide. Subjects include:

McGraw Hill Professional Bookstore
Publishes the most renowned and respected reference works in architecture, engineering, aviation, electronics, technical trades, and medicine, and is an industry leader in emerging fields such as robotics, telecommunications, and audio/video technology. Subjects include:

Springer
Buy academic journals, books and online media at Springer. Choose from thousands of scientific, technology medical and business titles and view our range of services for authors, booksellers and librarians. Subject areas include:

Thieme
Thieme, an international scientific and medical publisher, has produced high-quality products for physicians, scientists, technologists, students, and residents for nearly 120 years. Major specialty areas include neurosurgery, radiology, otolaryngology, orthopedics, ophthalmology, audiology, speech and hearing, complementary medicine, and chemistry.

Wiley-VCH
subsidiary of John Wiley & Sons

W.H. Freeman and Co., part of the Bedford, Freeman and Worth Publishing Group LLC
Publisher of high school, college, and career texts such as the classic introductory biochemistry texts of Lehninger and Stryer. Subjects include:

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