Cheminformatics-new

 
 Structure Elucidation

Spectra simulation, structure elucidation of chemicals

Tools

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

Databases

ResourceDeveloperProprietary or Public Domain?
ACD/NMR DatabasesACD/Labsproprietary
BMRB - Biological Magnetic Resonance Data BankBMRB project team, University of Wisconsinpublic domain
ChemGate (chemical structure search)John Wiley & Sons, Inc. and eMolecules, Inc.public domain
ChemSpiderRoyal Society of Chemistry, Cambridgepublic domain
CSD - Cambridge Structural DatabaseCambridge Crystallographic Data Centreproprietary
CSD Linker DatabaseChemical Computing Grouppublic domain
CSDS - Cambridge Structural Database SystemCambridge Crystallographic Data Centreproprietary
Database of Macromolecular MovementMark Gerstein, et al., Yale Universitypublic domain
GPCRDB - G Protein-Coupled Receptor Data BaseGPCRDB development teampublic domain
MMDB - Molecular Modeling Database (NCBI Structure)National Center for Biotechnology Information, NLM, NIHpublic domain
NCI DIS 3D - National Cancer Institute Drug Information System 3D structure databaseNCI (National Cancer Institute), NIHpublic domain
NIST Chemistry WebBookNISTpublic domain
NMRShiftDBnmrshiftdb2 development teampublic domain
SDBS - Spectral Database for Organic CompoundsNational Institute of Advanced Industrial Science and Technology (AIST), Japanpublic domain
Sigma-Aldrich - Chemical searchSigma-Aldrich Co. LLC.proprietary
SpecInfoJohn Wiley & Sons, Inc.proprietary
Spectral databaseUSEPA and US Air Forcepublic domain
Property/Activity Prediction

Prediction of physical and biological properties and activities of chemicals

Tools

ResourceDeveloperProprietary or Public Domain?
Accelrys Discovery Studio ("predictive science application for the Life Sciences")Accelrysproprietary
ACD/Tox SuiteACD/Labsproprietary
ADMET Predictor - Absorption, Distribution, Metabolism, Elimination, Toxicity PredictorSimulations Plus, Inc.proprietary
ALOGPS ("provides interactive on-line prediction of logP, water solubility and pKa(s) of compounds")Virtual Computational Chemistry Laboratorypublic domain
AutoDock (docking tools suite)The Scripps Research Institutepublic domain
Bioclipse ("workbench for the life sciences" based on Eclipse Rich Client Platform)Bioclipse development teampublic domain
CAESAR - Computer Assisted Evaluation of industrial chemical Substances According to RegulationsVEGApublic domain
CASEUltraMultiCase Inc.proprietary
ChemBioNavigator (visualization of chemical and biological space of molecular groups)University of Hamburg and BioSolveITpublic domain
Chemicalize (search chemical structures)ChemAxonpublic domain
CheS-Mapper ("Chemical Space Mapping and Visualization in 3D")Albert-Ludwigs-Universität Freiburg, Germany (M. Gutlein et al.)public domain
CORINA ("3D structure generator for small and medium sized, [...] molecules")Molecular Networks GmbHproprietary
Derek NexusLhasa Limitedproprietary
EPI - Estimation Program Interface Suite - suite of physical/chemical property and environmental fate estimation programsUSEPApublic domain
FlexXBioSolveITproprietary
HazardExpert ProCompuDrugproprietary
Jaguar ("ab initio electronic structure package")Schrödinger, LLCproprietary
Lazar - chemical toxicity predictionIn Silico Toxicology GmBHpublic domain
MOE - Molecular Operating EnvironmentChemical Computing Groupproprietary
MoKaMolecular Discovery Ltdproprietary
OncoLogic - Evaluate the carcinogenic potential of chemicalsUSEPApublic domain
QiKPropSchrodinger, LLCproprietary
QSAR ToolboxOrganisation for Economic Co-operation and Development and European Chemicals Agencyproprietary
Reaxys system (Search substances, reactions, citations, patents, etc.)Reaxys development teampublic domain
Sigma-Aldrich Structure Search (search chemical structures)Sigma-Aldrich Co. LLC.public domain
SPARC - SPARC Performs Automated Reasoning in ChemistryUSEPAproprietary
Spartan (molecular modeling package)WaveFunctionproprietary
SYBYL ("Molecular Modeling from Sequence through Lead Optimization")Certara, L.P. and Triposproprietary
TOPKAT - TOxicity Prediction by Komputer Assisted Technologyaccelrysproprietary
Toxtree (Estimatation of toxic hazard by applying a decision tree approach)Ideaconsult Ltdpublic domain

Databases

ResourceDeveloperProprietary or Public Domain?
AEGL - Acute Exposure Guideline LevelsUSEPApublic domain
Air Liquide Gas EncyclopediaAir Liquidepublic domain
Cambridge Structural DatabaseCambridge Crystallographic Data Centrepublic domain
CCRIS - Chemical Carcinogenesis Research Information SystemNLMpublic domain
ChemBankBroad Institutepublic domain
ChemIDplus AdvancedNLMpublic domain
ChemSpiderRoyal Society of Chemistry, Cambridgepublic domain
CICAD - Concise International Chemical Assessment DocumentsIPCS INCHEMpublic domain
CRC Handbook of Chemistry and PhysicsCRC Pressproprietary
CRC Handbook of Data on Organic CompoundsCRC Pressproprietary
DART - Developmental and Reproductive Toxicology DatabaseNLM, NIHpublic domain
DIPPR 801 DatabaseDIPPR, AIChEproprietary
DSSTox - Distributed Structure-Searchable ToxicityUSEPApublic domain
ECOTOX - ECOTOXicologyUSEPApublic domain
EFDB - Environmental Fate Data BaseSRC Incpublic domain
ERPG - Emergency Response Planning GuidelinesAIHApublic domain
GeneToxNLMpublic domain
GESTIS - International limit values for chemical agentsIFA - Institut fur Arbeitsschutzpublic domain
Howard's Handbook of Environmental Fate and Exposure Data for Organic ChemicalsPhilip Hall Howardproprietary
HSDB - Hazardous Substances Data BankNational Library of Medicinepublic domain
ICSC - International Chemical Safety CardsInternational Labour Organizationpublic domain
IIPP - Inert Ingredients in Pesticide ProductsUSEPApublic domain
ITER - International Toxicity Estimates for RiskNational Library of Medicinepublic domain
Kirk-Othmer Encyclopedia of Chemical TechnologyWiley Online Libraryproprietary
Lange's Handbook of ChemistryMcGraw-Hillproprietary
LOGKOW databaseSangster Research Laboratories, Canadapublic domain
Mackay's Handbook of Physical-Chemical Properties and Environmental Fate for Organic ChemicalsCRC Pressproprietary
Merck IndexMerck & Co Incpublic domain
MMG - Medical Management GuidelinesATSDR, CDCpublic domain
MSDS - Material Safety Data Sheets3E Companypublic domain
NIST Chemistry WebBookNISTpublic domain
NJ-HSFS - Right to Know Hazardous Substance Fact SheetsNJ Department of Healthpublic domain
NJ-RTKHSL - Right to Know Hazardous Substance ListNJ Department of Healthpublic domain
NLM ChemIDplus AdvancedNational Library of Medicinepublic domain
NPG - NIOSH Pocket Guide to Chemical HazardsCDC - NIOSHpublic domain
OChD - OSHA Occupational Chemical DatabaseOSHApublic domain
OChem - Online Chemical databaseeADMET GmbH, Germanypublic domain
PAC - Protective Action CriteriaUSDOEpublic domain
PHS - Public Health StatementsATSDR, CDCpublic domain
PHYSPROP - Physical Properties DatabaseSRCproprietary
Protective Action CriteriaEMI SIGpublic domain
PRS - Pesticide Reregistration StatusUSEPApublic domain
PSAP - Priority Substances Assessment ProgramHealth Canadapublic domain
PubChemNational Center for Biotechnology Information, NLM, NIHpublic domain
PubMedNational Center for Biotechnology Information, NLM, NIHpublic domain
REACH - Registration, Evaluation, Authorisation and Restriction of Chemical substancesEuropean Chemicals Agencypublic domain
Reaxys Chemistry DatabaseReaxysproprietary
RIVM reportsRIVMpublic domain
RTECS - Registry of Toxic Effects of Chemical SubstancesCDCproprietary
Scorecard Chemical ProfilesGoodGuidepublic domain
Sigma-Aldrich - Chemical searchSigma-Aldrich Co. LLC.proprietary
Spin Trap DatabaseNIEHSpublic domain
SRS - Substance Registry ServicesUSEPApublic domain
TEACH - Toxicity and Exposure Assessment for Children's HealthUSEPApublic domain
ToxCast - Toxicity ForecasterUSEPApublic domain
ToxFAQsATSDR, CDCpublic domain
ToxGuides™ATSDR, CDCpublic domain
TOXLINE - Toxicology Literature OnlineNational Library of Medicinepublic domain
ToxNetNational Library of Medicinepublic domain
ToxProfilesATSDR, CDCpublic domain
ToxRefDB - Toxicity Reference DatabaseUSEPApublic domain
TSCAInv - TSCA InventoryUSEPApublic domain
TSCATS - Toxic Substance Control Act Test Submission DatabaseSRC Incproprietray
Ullmann's Encyclopedia of Industrial ChemistryJohn Wiley & Sons, Incproprietary
WISER - Wireless Information System for Emergency RespondersNational Library of MedicinePublic Domain
Interaction/Reaction Modeling

Interaction and reaction modeling of chemicals

Tools

ResourceDeveloperProprietary or Public Domain?
CLIP - Closed-Loop Identification ProtocolRabitz Laboratory, Princeton Universityproprietary
COPASI - Complex Pathway Simulator ("successor of Gepasi")Virginia Bioinformatics Institute, Virginia Techpublic domain
Dynamic Signaling MapsHippron Physiomics Incproprietary
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)public domain
Gepasi (see COPASI)Virginia Bioinformatics Institute, Virginia Techpublic domain
Jaguar ("ab initio electronic structure package")Schrödinger, LLCproprietary
KEGG LIGAND databaseKanehisa Laboratories, Japanpublic domain
Macromodel ("program for molecular modeling")Schrödinger, LLCproprietary
METAPCMulticase Incproprietary
MetaSiteMolecular Discoveryproprietary
MeteorLhasa Limitedproprietary
MEXAlertCompuDrugproprietary
OmixPeter Drosteproprietary
PathwayLab - in silico pathway analysis toolInneticsproprietary
RetroMEXCompuDrugproprietary
Spartan (molecular modeling package)WaveFunctionproprietary