Links
"Vernetztes Studium - Chemie (VS-C)"
A project funded by the German Federal Minister of Education and Research (BMBF) including teaching material on Chemoinformatics.
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A collection of interesting links to Chemoinformatics and related topics (including all links mentioned in the Textbook).
- Introduction
- Representation of Chemical Compounds
- Representation of Chemical Reactions
- The Data
- Databases/Datasources
- Databases/Datasources
- Calculation of Physical and Chemical Data
- Calculation of Structure Descriptors
- Methods for Data Analysis
- Applications
2. Representation of Chemical Compounds
Available Software
3. Representation of Chemical Reactions
4. The Data
5. Databases/Datasources
Available Software
6. Structure Search Methods
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
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
Available Software
10. Applications
Available Software
Dr. Thomas Engel - Faculty for Chemistry and Pharmacy