Cheminformatics

 
Structure Elucidation

Spectra simulation, structure elucidation of chemicals

Computational Analysis Tools

ResourceDeveloper
ACD/NMR ExpertACD/Labs
ACD/NMR PredictorsACD/Labs
ACD/NMR Processor Academic Edition (processing of 1D and 2D NMR data)ACD/Labs
AMDIS - Automated MS Deconvolution and Identification SystemNIST
Bioclipse ("workbench for the life sciences" based on Eclipse Rich Client Platform)Bioclipse development team
ChemGate (chemical structure search)John Wiley & Sons, Inc. and eMolecules, Inc.
CheS-Mapper ("Chemical Space Mapping and Visualization in 3D")Albert-Ludwigs-Universität Freiburg, Germany (M. Gutlein et al.)
CSDS - Cambridge Structural Database SystemCambridge Crystallographic Data Centre
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)
GPUFRAGFOLD - Protein Structure Prediction toolBioinformatics Group, University College London
Jaguar ("ab initio electronic structure package")Schrödinger, LLC
MetworksThermo Scientific
Online SMILES Translator and Structure File GeneratorCADD Group, Chemical Biology Laboratory, NCI
ProcessIt NMRBio-Rad Laboratories
RasMol ("Molecular Graphics Visualisation Tool")RasMOL development team
Sigma-Aldrich Structure Search (search chemical structures)Sigma-Aldrich Co. LLC.
Spartan (molecular modeling package)WaveFunction
SYBYL ("Molecular Modeling from Sequence through Lead Optimization")Certara, L.P. and Tripos
THREADER (Protein Structure Prediction tool)Bioinformatics Group, University College London
TopSpin (NMR data analysis and acquisition and processing of NMR spectra)Bruker Corporation
VIDA (molecular modeling software)OpenEye Scientific Software Inc.

Information Portals and Databases

ResourceDeveloper
ACD/NMR DatabasesACD/Labs
BMRB - Biological Magnetic Resonance Data BankBMRB project team, University of Wisconsin
ChemGate (chemical structure search)John Wiley & Sons, Inc. and eMolecules, Inc.
ChemSpiderRoyal Society of Chemistry, Cambridge
CSD - Cambridge Structural DatabaseCambridge Crystallographic Data Centre
CSD Linker DatabaseChemical Computing Group
CSDS - Cambridge Structural Database SystemCambridge Crystallographic Data Centre
Database of Macromolecular MovementMark Gerstein, et al., Yale University
GPCRDB - G Protein-Coupled Receptor Data BaseGPCRDB development team
MMDB - Molecular Modeling Database (NCBI Structure)National Center for Biotechnology Information, NLM, NIH
NCI DIS 3D - National Cancer Institute Drug Information System 3D structure databaseNCI (National Cancer Institute), NIH
NIST Chemistry WebBookNIST
NMRShiftDBnmrshiftdb2 development team
SDBS - Spectral Database for Organic CompoundsNational Institute of Advanced Industrial Science and Technology (AIST), Japan
Sigma-Aldrich - Chemical searchSigma-Aldrich Co. LLC.
SpecInfoJohn Wiley & Sons, Inc.
Spectral databaseUSEPA and US Air Force
Property/Activity Prediction

Prediction of physical and biological properties and activities of chemicals

Computational Analysis Tools

ResourceDeveloper
Accelrys Discovery Studio ("predictive science application for the Life Sciences")Accelrys
ACD/Tox SuiteACD/Labs
ADMET Predictor - Absorption, Distribution, Metabolism, Elimination, Toxicity PredictorSimulations Plus, Inc.
ALOGPS ("provides interactive on-line prediction of logP, water solubility and pKa(s) of compounds")Virtual Computational Chemistry Laboratory
AutoDock (docking tools suite)The Scripps Research Institute
Bioclipse ("workbench for the life sciences" based on Eclipse Rich Client Platform)Bioclipse development team
CAESAR - Computer Assisted Evaluation of industrial chemical Substances According to RegulationsVEGA
CASEUltraMultiCase Inc.
ChemBioNavigator (visualization of chemical and biological space of molecular groups)University of Hamburg and BioSolveIT
Chemicalize (search chemical structures)ChemAxon
CheS-Mapper ("Chemical Space Mapping and Visualization in 3D")Albert-Ludwigs-Universität Freiburg, Germany (M. Gutlein et al.)
CORINA ("3D structure generator for small and medium sized, [...] molecules")Molecular Networks GmbH
Derek NexusLhasa Limited
EPI - Estimation Program Interface Suite - suite of physical/chemical property and environmental fate estimation programsUSEPA
FlexXBioSolveIT
HazardExpert ProCompuDrug
Jaguar ("ab initio electronic structure package")Schrödinger, LLC
Lazar - chemical toxicity predictionIn Silico Toxicology GmBH
MOE - Molecular Operating EnvironmentChemical Computing Group
MoKaMolecular Discovery Ltd
OncoLogic - Evaluate the carcinogenic potential of chemicalsUSEPA
QiKPropSchrodinger, LLC
QSAR ToolboxOrganisation for Economic Co-operation and Development and European Chemicals Agency
Reaxys system (Search substances, reactions, citations, patents, etc.)Reaxys development team
Sigma-Aldrich Structure Search (search chemical structures)Sigma-Aldrich Co. LLC.
SPARC - SPARC Performs Automated Reasoning in ChemistryUSEPA
Spartan (molecular modeling package)WaveFunction
SYBYL ("Molecular Modeling from Sequence through Lead Optimization")Certara, L.P. and Tripos
TOPKAT - TOxicity Prediction by Komputer Assisted Technologyaccelrys
Toxtree (Estimatation of toxic hazard by applying a decision tree approach)Ideaconsult Ltd

Information Portals and Databases

ResourceDeveloper
AEGL - Acute Exposure Guideline LevelsUSEPA
Air Liquide Gas EncyclopediaAir Liquide
Cambridge Structural DatabaseCambridge Crystallographic Data Centre
CCRIS - Chemical Carcinogenesis Research Information SystemNLM
ChemBankBroad Institute
ChemIDplus AdvancedNLM
ChemSpiderRoyal Society of Chemistry, Cambridge
CICAD - Concise International Chemical Assessment DocumentsIPCS INCHEM
CRC Handbook of Chemistry and PhysicsCRC Press
CRC Handbook of Data on Organic CompoundsCRC Press
DART - Developmental and Reproductive Toxicology DatabaseNLM, NIH
DIPPR 801 DatabaseDIPPR, AIChE
DSSTox - Distributed Structure-Searchable ToxicityUSEPA
ECOTOX - ECOTOXicologyUSEPA
EFDB - Environmental Fate Data BaseSRC Inc
ERPG - Emergency Response Planning GuidelinesAIHA
GeneToxNLM
GESTIS - International limit values for chemical agentsIFA - Institut fur Arbeitsschutz
Howard's Handbook of Environmental Fate and Exposure Data for Organic ChemicalsPhilip Hall Howard
HSDB - Hazardous Substances Data BankNational Library of Medicine
ICSC - International Chemical Safety CardsInternational Labour Organization
IIPP - Inert Ingredients in Pesticide ProductsUSEPA
ITER - International Toxicity Estimates for RiskNational Library of Medicine
Kirk-Othmer Encyclopedia of Chemical TechnologyWiley Online Library
Lange's Handbook of ChemistryMcGraw-Hill
LOGKOW databaseSangster Research Laboratories, Canada
Mackay's Handbook of Physical-Chemical Properties and Environmental Fate for Organic ChemicalsCRC Press
Merck IndexMerck & Co Inc
MMG - Medical Management GuidelinesATSDR, CDC
MSDS - Material Safety Data Sheets3E Company
NIST Chemistry WebBookNIST
NJ-HSFS - Right to Know Hazardous Substance Fact SheetsNJ Department of Health
NJ-RTKHSL - Right to Know Hazardous Substance ListNJ Department of Health
NLM ChemIDplus AdvancedNational Library of Medicine
NPG - NIOSH Pocket Guide to Chemical HazardsCDC - NIOSH
OChD - OSHA Occupational Chemical DatabaseOSHA
OChem - Online Chemical databaseeADMET GmbH, Germany
PAC - Protective Action CriteriaUSDOE
PHS - Public Health StatementsATSDR, CDC
PHYSPROP - Physical Properties DatabaseSRC
Protective Action CriteriaEMI SIG
PRS - Pesticide Reregistration StatusUSEPA
PSAP - Priority Substances Assessment ProgramHealth Canada
PubChemNational Center for Biotechnology Information, NLM, NIH
PubMedNational Center for Biotechnology Information, NLM, NIH
REACH - Registration, Evaluation, Authorisation and Restriction of Chemical substancesEuropean Chemicals Agency
Reaxys Chemistry DatabaseReaxys
RIVM reportsRIVM
RTECS - Registry of Toxic Effects of Chemical SubstancesCDC
Scorecard Chemical ProfilesGoodGuide
Sigma-Aldrich - Chemical searchSigma-Aldrich Co. LLC.
Spin Trap DatabaseNIEHS
SRS - Substance Registry ServicesUSEPA
TEACH - Toxicity and Exposure Assessment for Children's HealthUSEPA
ToxCast - Toxicity ForecasterUSEPA
ToxFAQsATSDR, CDC
ToxGuides™ATSDR, CDC
TOXLINE - Toxicology Literature OnlineNational Library of Medicine
ToxNetNational Library of Medicine
ToxProfilesATSDR, CDC
ToxRefDB - Toxicity Reference DatabaseUSEPA
TSCAInv - TSCA InventoryUSEPA
TSCATS - Toxic Substance Control Act Test Submission DatabaseSRC Inc
Ullmann's Encyclopedia of Industrial ChemistryJohn Wiley & Sons, Inc
WISER - Wireless Information System for Emergency RespondersNational Library of Medicine
Interaction/Reaction Modeling

Interaction and reaction modeling of chemicals

Computational Analysis Tools

ResourceDeveloper
CLIP - Closed-Loop Identification ProtocolRabitz Laboratory, Princeton University
COPASI - Complex Pathway Simulator ("successor of Gepasi")Virginia Bioinformatics Institute, Virginia Tech
Dynamic Signaling MapsHippron Physiomics Inc
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)
Gepasi (see COPASI)Virginia Bioinformatics Institute, Virginia Tech
Jaguar ("ab initio electronic structure package")Schrödinger, LLC
Macromodel ("program for molecular modeling")Schrödinger, LLC
METAPCMulticase Inc
MetaSiteMolecular Discovery
MeteorLhasa Limited
MEXAlertCompuDrug
OmixPeter Droste
PathwayLab - in silico pathway analysis toolInnetics
RetroMEXCompuDrug
Spartan (molecular modeling package)WaveFunction

Information Portals and Databases

ResourceDeveloper
KEGG LIGAND databaseKanehisa Laboratories, Japan