ChemoPy: freely available python package for computational biology and chemoinformatics

• 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; 1460-2059
• DOI: 10.1093/bioinformatics/btt105

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. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.