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