Cheminformatics » Environmental Bioinformatics Knowledge Base


  Structure Elucidation

Spectra simulation, structure elucidation of chemicals

Computational Analysis Tools

Information Portals and Databases

Resource Developer
ACD/NMR Databases ACD/Labs
BMRB – Biological Magnetic Resonance Data Bank BMRB project team, University of Wisconsin
ChemGate (chemical structure search) John Wiley & Sons, Inc. and eMolecules, Inc.
ChemSpider Royal Society of Chemistry, Cambridge
CSD – Cambridge Structural Database Cambridge Crystallographic Data Centre
CSD Linker Database Chemical Computing Group
CSDS – Cambridge Structural Database System Cambridge Crystallographic Data Centre
Database of Macromolecular Movement Mark Gerstein, et al., Yale University
GPCRDB – G Protein-Coupled Receptor Data Base GPCRDB 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 database NCI (National Cancer Institute), NIH
NIST Chemistry WebBook NIST
NMRShiftDB nmrshiftdb2 development team
SDBS – Spectral Database for Organic Compounds National Institute of Advanced Industrial Science and Technology (AIST), Japan
Sigma-Aldrich – Chemical search Sigma-Aldrich Co. LLC.
SpecInfo John Wiley & Sons, Inc.
Spectral database USEPA and US Air Force

Property/Activity Prediction

Prediction of physical and biological properties and activities of chemicals

Computational Analysis Tools

Resource Developer
Accelrys Discovery Studio (“predictive science application for the Life Sciences”) Accelrys
ACD/Tox Suite ACD/Labs
ADMET Predictor – Absorption, Distribution, Metabolism, Elimination, Toxicity Predictor Simulations 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 Regulations VEGA
CASEUltra MultiCase 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 Nexus Lhasa Limited
EPI – Estimation Program Interface Suite – suite of physical/chemical property and environmental fate estimation programs USEPA
FlexX BioSolveIT
HazardExpert Pro CompuDrug
Jaguar (“ab initio electronic structure package”) Schrödinger, LLC
Lazar – chemical toxicity prediction In Silico Toxicology GmBH
MOE – Molecular Operating Environment Chemical Computing Group
MoKa Molecular Discovery Ltd
OncoLogic – Evaluate the carcinogenic potential of chemicals USEPA
QiKProp Schrodinger, LLC
QSAR Toolbox Organisation 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 Chemistry USEPA
Spartan (molecular modeling package) WaveFunction
SYBYL (“Molecular Modeling from Sequence through Lead Optimization”) Certara, L.P. and Tripos
TOPKAT – TOxicity Prediction by Komputer Assisted Technology accelrys
Toxtree (Estimatation of toxic hazard by applying a decision tree approach) Ideaconsult Ltd

Information Portals and Databases

Resource Developer
AEGL – Acute Exposure Guideline Levels USEPA
Air Liquide Gas Encyclopedia Air Liquide
Cambridge Structural Database Cambridge Crystallographic Data Centre
CCRIS – Chemical Carcinogenesis Research Information System NLM
ChemBank Broad Institute
ChemIDplus Advanced NLM
ChemSpider Royal Society of Chemistry, Cambridge
CICAD – Concise International Chemical Assessment Documents IPCS INCHEM
CRC Handbook of Chemistry and Physics CRC Press
CRC Handbook of Data on Organic Compounds CRC Press
DART – Developmental and Reproductive Toxicology Database NLM, NIH
DIPPR 801 Database DIPPR, AIChE
DSSTox – Distributed Structure-Searchable Toxicity USEPA
ECOTOX – ECOTOXicology USEPA
EFDB – Environmental Fate Data Base SRC Inc
ERPG – Emergency Response Planning Guidelines AIHA
GeneTox NLM
GESTIS – International limit values for chemical agents IFA – Institut fur Arbeitsschutz
Howard’s Handbook of Environmental Fate and Exposure Data for Organic Chemicals Philip Hall Howard
HSDB – Hazardous Substances Data Bank National Library of Medicine
ICSC – International Chemical Safety Cards International Labour Organization
IIPP – Inert Ingredients in Pesticide Products USEPA
ITER – International Toxicity Estimates for Risk National Library of Medicine
Kirk-Othmer Encyclopedia of Chemical Technology Wiley Online Library
Lange’s Handbook of Chemistry McGraw-Hill
LOGKOW database Sangster Research Laboratories, Canada
Mackay’s Handbook of Physical-Chemical Properties and Environmental Fate for Organic Chemicals CRC Press
Merck Index Merck & Co Inc
MMG – Medical Management Guidelines ATSDR, CDC
MSDS – Material Safety Data Sheets 3E Company
NIST Chemistry WebBook NIST
NJ-HSFS – Right to Know Hazardous Substance Fact Sheets NJ Department of Health
NJ-RTKHSL – Right to Know Hazardous Substance List NJ Department of Health
NLM ChemIDplus Advanced National Library of Medicine
NPG – NIOSH Pocket Guide to Chemical Hazards CDC – NIOSH
OChD – OSHA Occupational Chemical Database OSHA
OChem – Online Chemical database eADMET GmbH, Germany
PAC – Protective Action Criteria USDOE
PHS – Public Health Statements ATSDR, CDC
PHYSPROP – Physical Properties Database SRC
Protective Action Criteria EMI SIG
PRS – Pesticide Reregistration Status USEPA
PSAP – Priority Substances Assessment Program Health Canada
PubChem National Center for Biotechnology Information, NLM, NIH
PubMed National Center for Biotechnology Information, NLM, NIH
REACH – Registration, Evaluation, Authorisation and Restriction of Chemical substances European Chemicals Agency
Reaxys Chemistry Database Reaxys
RIVM reports RIVM
RTECS – Registry of Toxic Effects of Chemical Substances CDC
Scorecard Chemical Profiles GoodGuide
Sigma-Aldrich – Chemical search Sigma-Aldrich Co. LLC.
Spin Trap Database NIEHS
SRS – Substance Registry Services USEPA
TEACH – Toxicity and Exposure Assessment for Children’s Health USEPA
ToxCast – Toxicity Forecaster USEPA
ToxFAQs ATSDR, CDC
ToxGuides™ ATSDR, CDC
TOXLINE – Toxicology Literature Online National Library of Medicine
ToxNet National Library of Medicine
ToxProfiles ATSDR, CDC
ToxRefDB – Toxicity Reference Database USEPA
TSCAInv – TSCA Inventory USEPA
TSCATS – Toxic Substance Control Act Test Submission Database SRC Inc
Ullmann’s Encyclopedia of Industrial Chemistry John Wiley & Sons, Inc
WISER – Wireless Information System for Emergency Responders National Library of Medicine

Interaction/Reaction Modeling

Interaction and reaction modeling of chemicals

Computational Analysis Tools

Information Portals and Databases

Resource Developer
KEGG LIGAND database Kanehisa Laboratories, Japan