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

1. Introduction

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

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

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

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