SUBJECT APPENDICES DRUG DISCOVERY INFORMATICS REGISTRATION SYSTEMS AND UNDERLYING TOOLKITS (APPENDICES 1 AND 2) Appendix 1: DRUG, MOLECULAR REGISTRATION SYSTEMS, AND CHEMISTRY DATA CARTRIDGES Product Company Page Website Isentris, MDL- MDL 171 http://www.mdli.com Base, ISIS- Base ChemOffice Cambridgesoft 73 http://www.cambridgesoft.com Cambridgesoft CambridgeSoft 73 http://www.cambridgesoft.com/solutions/ Enterprise Solutions ActivityBase IDBS 152 http://www.idbs.com/products/abase/ Accord Accelrys 51 http://www.accelrys.com AUSPYX Tripos 261 http://www.tripos.com CBIS ChemInnovation 103 http://www.cheminnovation.com/ (Chemical and Software Biological Informatics Systems) ACD/SpecDB ACD Labs 59 http://www.acdlabs.com (Spectral Data Management System) - Analytical data capture tools Super Package BioByte 71 http://www.biobyte.com/index.html /THOR (Daylight) JChem ChemAxon 89 http://www.chemaxon.com Cartridge Software for Infochem 156 http://www.infochem.de/en/company/ Chemical index.shtml databases and chemical data processes 271 272 CHEMOINFORMATICS The InfoChem Infochem 156 http://www.infochem.de/eng/index.htm Chemistry Cartridge for Oracle Molecular Collaborative 115 http://www.collaborativedrug.com/ Databank Drug Discovery DayCart Daylight 123 http://www.daylight.com/ Chemical Information Systems, Inc. CHED, TimTec 254 http://software.timtec.net/ Chemdbsoft MDL Isentris MDL 171 http://www.mdli.com platform (ISIS Base), ChemBio AE, AssayExplorer Appendix 2: CHEMOINFORMATICS TOOLKITS TO DEVELOP APPLICATIONS Product Company Page Website OEChem Open Eye 194 http://www.eyesopen.com/ Marvin ChemAxon 87 http://www.chemaxon.com/ Calculator ChemAxon 88 http://www.chemaxon.com Plugins JChem Base ChemAxon 89 http://www.chemaxon.com MOE Chemical 98 http://www.chemcomp.com/ (Molecular Computing Operating Group Environment) CORINA ϩ Molecular 187 http://www.mol-net.com other products Networks GmbH MetaDrug GeneGo 141 http://www.genego.com SUBJECT APPENDICES 273 CONTENT DATABASES (APPENDICES 3–7) Appendix 3: COMPOUND AVAILABILITY DATABASES Product Company Page Website Available MDL 171 http://www.mdli.com Chemicals Directory (ACD, ACD screen) ChemACX Cambridgesoft 73 http://www.cambridgesoft.com/databases/ ChemMatrix ChemNavigator 109 http://www.chemnavigator.com Technology PubChem PubChem 203 http://pubchem.ncbi.nlm.nih.gov/ Molecular Collaborative Drug 115 http://www.collaborativedrug.com/ Databank Discovery Appendix 4: SAR DATABASE Product Company Page Website Kinase Jubilant Biosys 164 http://www.jubilantbiosys.com/ ChemBioBase Gene family GVK-BIO 144 http://www.gvkbio.com/ databases LUCIA Eidogen-Sertanty 128 http://www.eidogen-sertanty.com/ TIP (Target Eidogen-Sertanty 127 http://www.eidogen-sertanty.com/ Informatics Platform) GPCR Jubilant Biosys 164 http://www.jubilantbiosys.com/ Annotator PubChem PubChem 203 http://pubchem.ncbi.nlm.nih.gov/ CDD Molecular Collaborative Drug 115 http://www.collaborativedrug.com/ Databank Discovery MDDR MDL 175 http://www.mdli.com (MDL Drug Data Report) 274 CHEMOINFORMATICS Appendix 5: CHEMICAL REACTION DATABASES Product Company Page Website SPREZZI InfoChem 156 http://www.infochem.de/en/company/ index.shtml SPRESIweb InfoChem 158 http://www.infochem.de/en/company/ index.shtml Beilstein, MDL 175 http://www.mdli.com Crossfire, SPORE, ChemInform Reaction Library, ORGSYN, etc. LUCIA Sertanty (previously 128 http://www.eidogen-sertanty.com Libraria) Arthur Symyx 248 http://www.symyx.com SciFinder Chemistry Abstract 80 http://www.cas.org, Services http://www.cas.org/prod.html CA File Chemistry Abstract 80 http://www.cas.org, Services http://www.cas.org/prod.html CAS Registry Chemistry Abstract 80 http://www.cas.org, Services http://www.cas.org/prod.html CA on CD Chemistry Abstract 81 http://www.cas.org, Services http://www.cas.org/prod.html CAplus Chemistry Abstract 81 http://www.cas.org, Services http://www.cas.org/prod.html MARPAT – Chemistry Abstract 81 http://www.cas.org, CAS Markush Services http://www.cas.org/prod.html database CASREACT Chemistry Abstract 81 http://www.cas.org, Services http://www.cas.org/prod.html CHEMCATS Chemistry Abstract 82 http://www.cas.org, File Services http://www.cas.org/prod.html RxD – GVK BIO 144 http://www.gvkbio.com/ Chemical Reaction Database SUBJECT APPENDICES 275 Appendix 6: PATENT DATABASES Product Company Page Website Derwent Thompson 175 http://www.mdli.com /MDL MDL Patent MDL 176 http://www.mdli.com Chemistry Database CAplus Chemistry 81 http://www.cas.org, Abstract http://www.cas.org/prod.html Services MARPAT – CAS Chemistry 81 http://www.cas.org, Markush Abstract http://www.cas.org/prod.html database Services Appendix 7: OTHER COMPOUND AND DRUG DATABASES Product Company Page Website MDDR Prous/MDL 175 http://www.mdli.com (MDL Drug Data Report), DiscoveryGate, OHS Reference, xPharm, etc. MetaCore GeneGo 140 http://www.genego.com MCD – Medichem GVK BIO 144 http://www.gvkbio.com/ Database TID – Target GVK BIO 145 http://www.gvkbio.com/ inhibitor databases PKD – GVK BIO 145 http://www.gvkbio.com/ Pharmacokinetic PPID – Protein- GVK BIO 145 http://www.gvkbio.com/ Protein interactions PathArt© Jubilant Biosys 164 http://www.jubilantbiosys.com/ Nitrilase and Jubilant Biosys 165 http://www.jubilantbiosys.com/ Nitrile Hydratase Knowledgebase Cambridgesoft CambridgeSoft 75 http://www.cambridgesoft.com/databases/ databases Global Major InfoChem 158 http://www.infochem.de/en/company/ Reference Works (and MDL) index.shtml 276 CHEMOINFORMATICS DRUG, MOLECULE, AND PROTEIN VISUALIZATION (APPENDICES 8–10) Appendix 8: CHEMICAL DRAWING, STRUCTURE VIEWING AND MODELING PACKAGES Product Company Page Website Chemdraw (8.0) CambridgeSoft 73 http://www.cambridgesoft.com ChemOffice CambridgeSoft 73 http://www.cambridgesoft.com HyperChem Web HyperCube 149 http://www.hyper.com/default.htm Viewer Chemlab Scinova 224 http://www.scinovaindia.com/ Technologies ArgusLab Planaria-Software 202 http://www.planaria-software.com/ RasMol – Academic 211 http://www.umass.edu/microbio/rasmol/ Protein Explorer (non-commercial) Marvin ChemAxon 87 http://www.chemaxon.com Chem-4D ChemInnovation 103 http://www.cheminnovation.com/ Software Chemsite ChemInnovation 104 http://www.cheminnovation.com/ Software Cerius2 Accelrys 51 http://www.accelrys.com Discovery Studio ViewerPro PyMol 0.92 PyMol 208 http://www.pymol.org Chemical TimTec 254 http://software.timtec.net/ Database Management Software ISIS-Draw MDL 173 http://www.mdli.com (MDL Draw) Chime plug-in MDL 211 http://www.mdli.com (Ras-Mol) Sybyl-base Tripos 259 http://www.tripos.com/ Appendix 9: DATA ANALYSIS AND MINING TOOLS Product Company Page Website Pipeline Pilot SciTegic 226 http://www.scitegic.com/products_ services/pipeline_pilot.htm Prometheus Scinova Technologies 224 http://www.scinovaindia.com/ Discovery Studio Accelrys 52 http://www.accelrys.com CombiMat 2.0 Accelrys 51 http://www.accelrys.com Screen Chemaxon 90 http://www.chemaxon.com/ SUBJECT APPENDICES 277 JKlustor Chemaxon 90 http://www.chemaxon.com/ Reactor Chemaxon 90 http://www.chemaxon.com/ Fragmentor Chemaxon 90 http://www.chemaxon.com/ Insight II Accelrys 51 http://www.accelrys.com STS (Synthesis Tree Infochem 158 http://www.infochem.de/en/company/ Search) index.shtml CLASSIFY Infochem 157 http://www.infochem.de/en/company/ index.shtml IC-Map Infochem 157 http://www.infochem.de/en/company/ index.shtml The ICFSE (Infochem Infochem 157 http://www.infochem.de/en/company Fast Search Engine) index.shtml Filter, Omega, ROCS, Open Eye 194 http://www.eyesopen.com/ SMACK, etc. DiverseSolutions Tripos 262 http://www.tripos.com/ Spotfire DecisionSite Spotfire 236 http://www.spotfire.com Diversity Analysis, Barnard 68 http://www.bci.gb.com/ Cluster Analysis Chemical Information Ltd. (BCI); CAChe, Fujitsu 137 http://us.fujitsu.com/biosciences BioMedCAChe Biosciences Group Merlin (exploratory Daylight 123 http://www.daylight.com/ data analysis tools) Chemical Information Systems, Inc. Thor Daylight 123 http://www.daylight.com/ (a database system Chemical based on Daylight’s Information SMILES notation) Systems, Inc. Appendix 10: SMALL MOLECULE – PROTEIN VISUALIZATION TOOLS Product Company Page Website RasMol University of 211 http://www.umass.edu/micro Massachusetts bio/rasmol/ Protein US National Science 211 http://molvis.sdsc.edu/protex Explorer Foundation pl/frntdoor.htm 3-Dimensional ChemNavigator 109 http://www.chemnavigator.com Protein-Ligand Map (3-DPL) Eve (Eidogen Eidogen-Sertanty 128 http://www.eidogen-sertanty.com/ Visualization Environment)TM 278 CHEMOINFORMATICS PyMOL PyMOL 208 http://www.pymol.org; hosted at: http://pymol.sourceforge.net/ 3-D molecular Chimera 112 http://www.cgl.ucsf.edu/chi visualization mera/index.html program Molsmart – Barnard Chemical 68 http://www.bci.gb.com/ converts MDL Information Ltd. to Daylight (BCI); formats MOE Chemical Computing 98 http://www.chemcomp.com/ (Molecular Group Operating Environment) MDL Sculpt MDL 174 http://www.mdli.com MODELING AND ALGORITHMS (APPENDICES 11–17) Appendix 11: MOLECULAR DESCRIPTORS Product Company Page Website DRAGON Milano Chemometrics and QSAR 180 http://www.disat.unimib.it/chm/ Research Group MOBYDIGS Milano Chemometrics and QSAR 181 http://www.disat.unimib.it/chm/ Research Group KOALA Milano Chemometrics and QSAR 181 http://www.disat.unimib.it/chm/ Research Group DOLPHIN Milano Chemometrics and QSAR 181 http://www.disat.unimib.it/chm/ Research Group Chemical Barnard Chemical 68 http://www.bci.gb.com/ Structure Information Ltd. (BCI) Fragments and Fingerprinting. Calculator Chemaxon 88 http://www.chemaxon.com/