Textbook - Interesting Websites

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Learning Objectives Essentials Interesting Websites Tutorials Comments Input-form Textbook Comments	1. Introduction 2. Representation of Chemical Compounds 3. Representation of Chemical Reactions 4. The Data 5. Databases/Datasources 6. Structure Search Methods 7. Calculation of Physical and Chemical Data 8. Calculation of Structure Descriptors 9. Methods for Data Analysis 10. Applications
	2. Representation of Chemical Compounds SMILES: http://www.daylight.com Molfile: http://www.mdli.com PDB Format Description: http://www.rcsb.org Chemical Markup Language: http://www.xml-cml.org/ Available Software http://www.cambridgesoft.com http://www.mol-net.de http://www.tripos.com http://www.mdli.com 3. Representation of Chemical Reactions 4. The Data SPSS - applicable in a wide range of engineering tasks. More details are available at http://www.spssscience.com/sigmastat/index.cfm The Unscrambler family from CAMO is specially designed by chemometricians. However, this package is also applicable in a wide range of engineering tasks. http://www.camo.no/p2_tuf.htm The SIMCA family from Umetrics - http://www.umetrics.com ELECTRAS - web-based data analysis system. The software supports 2 x 2 different modes of action: the modes for expert and novice engineers and the modes for expert and novice computational chemists. http://www2.chemie.uni-erlangen.de/projects/eDAS/index.html SONNIA - KSOM and CPG neural networks. The key features are robustness of training and excellent visualization capabilities. http://www.mol-net.de 5. Databases/Datasources http://www.stn-international.de http://info.cas.org http://www.ccdc.cam.ac.uk/prods/csd/csd.html http://pir.georgetown.edu/pirwww/dbinfo/resid.html http://www.thomson.com/scientific/scientific.jsp Available Software STN, STN Easy, SciFinder: http://www.cas.org/prod.html SciFinder Scholar: http://www.cas.org/SCIFINDER/SCHOLAR2002 (access only with license agreement) CrossFire Commander, AutoNom: http://www.mimas.ac.uk/crossfire/download.html 6. Structure Search Methods http://www2.chemie.uni-erlangen.de http://dtp.nci.nih.gov/docs/3D _database/structural_information/structural_data.html http://cactus.nci.nih.gov/ncidb2/download.html http://www.daylight.com http://www.queryplus.com http://www.isinet.com/isi/hot/essays/chemicalliterature/15.html http://citeseer.nj.nec.com/santini99similarity.html http://www.mol-net.de http://www.tripos.com Available Software DayCartTM is a software cartridge which offers a range of operation on an Oracle database, such as complete structure, similarity, and substructure search. The software can be obtained from Daylight Chemical Information Systems, Inc. (Mission Viejo CA); URL: http://www.daylight.com CACTVS is a chemical information system which provides 2D and 3D complete structure, substructure, and similarity search on plane files of structures. The software can be obtained from Molecular Networks GmbH (Erlangen, Germany); URL: http://www.mol-net.de C@ROL is a web-based warehouse with possibilities for full structure, substructure, and similarity search. The software can be obtained from Molecular Networks GmbH (Erlangen, Germany); URL: http://www.mol-net.de CORINA and CONCORD are 3D-builder programs which can be obtained from Molecular Networks GmbH (Erlangen, Germany) URL; URL: http://www.mol-net.de - and from Tripos, Inc., St. Louis, MO, USA; URL: http://www.tripos.com 7. Calculation of Physical and Chemical Data http://www.nist.gov/srd/thermo.htm http://www2.chemie.uni-erlangen.de/software/petra/index.html http://www.mol-net.de NIH Center for Molecular Modeling: http://cmm.info.nih.gov/ Molecular mechanics across chemistry: http://franklin.chm.colostate.edu/mmac/ Chemistry and biology applications on Linux: http://SAL.KachinaTech.COM/Z/2/ Software used in molecular modeling and molecular dynamics: http://www.ahpcc.unm.edu/~aroberts/main/mol__mod__software.htm A molecular dynamics primer with examples in Fortran90: http://www.fisica.uniud.it/~ercolessi/md/ Available Software TINKER A molecular modeling and simulation package with various implemented force field parameterizations. Free of charge for academic use. Available for different platforms. http://dasher.wustl.edu/tinker gOpenMol Visualization and analysis of structure and dynamics simulation results. Free of charge for academic use. Available for different platforms. Imports TINKER results and accepts various file formats. http://www.csc.fi/gopenmol/ DYNAMO A Fortran90 library for the simulation of molecular systems using molecular mechanics (MM) and hybrid quantum mechanics (QM)/MM potential energy functions http://www.ibs.fr/ext/labos/LDM/projet6/ MOSCITO Molecular dynamics simulation package with various force field implementations, special support for AMBER. Parallel version and X11 trajectory viewer available. http://ganter.chemie.uni-dortmund.de/MOSCITO/ 8. Calculation of Structure Descriptors ADAPT (QSAR program including descriptor generation, variable selection, and modeling); P.C. Jurs, PennState University, University Park, PA 16802, USA: http://research.chem.psu.edu/pcjgroup/ADAPT.html ASP (quantitative similarity calculation based on molecular shape, electrostatic potentials, and lipophilic information; within the TSAR3D package); Accelrys Inc.: http://www.accelrys.com/products/tsar/asp.html AUTOCORR; Molecular Networks GmbH, Nägelsbachstrasse 25, D-91052 Erlangen, Germany: http://www.mol-net.de/ CODESSA (calculation of a series of different descriptors including quantum chemical descriptors); Semichem Inc. - 7204 Mullen, Shawnee, KS 66216, USA: http://www.semichem.com CONCORD; TRIPOS, Inc., 1699 South Hanley Road, St. Louis, MO 63144, USA: http://www.tripos.com CORINA (3D coordinates generator); J. Gasteiger, Computer-Chemie-Centrum, University Erlangen-Nürnberg, Nägelsbachstrasse 25, D-91052 Erlangen, Germany: http://www2.chemie.uni-erlangen.de/ DRAGON (calculation of a broad range of descriptors - topological, geometrical, WHIM, 3D-MoRSE descriptors, molecular profiles, etc.); R. Todeschini, distributed by Talete srl, via Pisani 13, 20124 Milano, Italy: http://www.disat.unimib.it/chm GALAXY; AM Technologies, 14785 Omicron Drive, Texas Research Park, San Antonio, TX 78245, USA: http://www.am-tech.com GRID (calculation of the GRID empirical force field at grid points); Peter Goodford, Molecular Discovery Ltd., West Way House, Elms Parade, Oxford OX2 9LL, UK: http://www.moldiscovery.com/ HASL: http://www.eslc.vabiotech.com/hasl/ or http://www.edusoft-lc.com HINT: http://www.eslc.vabiotech.com/hint HYBOT-Plus (hydrogen bonding thermodynamics, calculation of local and molecular physicochemical descriptors): http://www.timtec.net/software/hybot-plus.htm JOELib: http://joelib.sourceforge.net MOE; Chemical Computing Group Inc.: http://www.chemcomp.com Molconn-Z: http://www.eslc.vabiotech.com/molconn/manuals/310s/preface1.html Molinspiration (calculation of log P (fragment-based method + correction factors), molecular polar surface area TPSA (Ertl), "Rule of 5" (Lipinski), number of rotatable bonds, and a drug-likeness index): http://www.molinspiration.com PENGUINS; Molecular Discovery Ltd., West Way House, Elms Parade, Oxford OX2 9LL, UK: http://www.moldiscovery.com/ PETRA (calculation of physicochemical parameters); Molecular Networks GmbH, Nägelsbachstrasse 25, D-91052 Erlangen, Germany: http://www.mol-net.de/ VolSurf; Molecular Discovery Ltd., West Way House, Elms Parade, Oxford OX2 9LL, UK: http://www.moldiscovery.com/ Further information about software for computer aided drug design (CADD) is available at the website http://www.netsci.org/Resources/Software/Modeling/CADD/. 9. Methods for Data Analysis http://www2.chemie.uni-erlangen.de/projects/eDAS/index.html (Electronic Data Analysis Service, Computer-Chemie-Centrum, University of Erlangen-Nürnberg) Available Software Weka (Machine Learning Software in Java); Department of Computer Science, University of Waikato; http://www.cs.waikato.ac.nz/~ml/weka/index.html SNNS (Stuttgart Neural Network Simulator); Wilhelm-Schickard-Institut für Informatik, University of Tübingen; http://www-ra.informatik.uni-tuebingen.de/SNNS/ GAlib (C++ Library of Genetic Algorithm Components), Massachusetts Institute of Technology; http://lancet.mit.edu/ga/ 10. Applications http://research.chem.psu.edu/pcjgroup Available Software (log P) ALOGP98 : http://www.accelrys.com MedChem (CLOP): http://www.daylight.com KOWWIN: http://esc.syrres.com XLOGP: ftp://ftp2.ipc.pku.edu.cn/pub/software/xlogp http://www.acdlabs.com/ilab http://www.bio-rad.com http://www.chemicalconcepts.com/p111.htm http://www2.chemie.uni-erlangen.de/services/telespec/index.html http://www.cambridgesoft.com http://www2.chemie.uni-erlangen.de/software/eros/index.html http://www2.chemie.uni-erlangen.de/software/cora/index.html http://www2.chemie.uni-erlangen.de/software/wodca/index.html http://www.expasy.ch http://www.genome.ad.jp/kegg/ http://www.cmbi.kun.nl/cheminf/lhasa http://home.t-online.de/home/kubinyi/lectures.html http://www.netsci.org/Science/Compchem/index.html
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Markus Sitzmann Thomas Engel 2003	Contact: Thomas Engel last update: 2003-10-19