ChemoPy: freely available python package for computational biology and chemoinformatics

Motivation: Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python...

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Bibliographic Details
Published in:Bioinformatics Vol. 29; no. 8; pp. 1092 - 1094
Main Authors: Cao, Dong-Sheng, Xu, Qing-Song, Hu, Qian-Nan, Liang, Yi-Zeng
Format: Journal Article
Language:English
Published: England 15.04.2013
Subjects:
Bioinformatics
Computational Biology - methods
Databases, Chemical
Drug Design
Drugs
Fingerprints
Keys
Ligands
Packages
Pharmaceutical Preparations - chemistry
Quantum chemistry
Software
Topology
ISSN:1367-4803, 1367-4811, 1367-4811, 1460-2059
Online Access:Get full text
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Summary:Motivation: Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. Availability: The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Contact:  yizeng_liang@263.net Supplementary information:  Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btt105