ChemoPy: freely available python package for computational biology and chemoinformatics
ChemoPy: freely available python package for computational biology and chemoinformatics
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ChemoPy：用于计算生物学和化学信息学的免费 Python 包
DOI：
10.1093/bioinformatics/btt105
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发表时间：
2013-04-15
期刊：
影响因子：
5.8
通讯作者：
Liang, Yi-Zeng
中科院分区：
文献类型：
--
作者：
Cao, Dong-Sheng;Xu, Qing-Song;Liang, Yi-Zeng
动机
小分子的分子表征已被常规地用于QSAR/SAR、虚拟筛选、数据库检索、排序、药物ADME/T预测和其他药物发现过程。为了促进对药物分子的广泛研究，我们开发了一个免费提供的开源Python包，称为Python中的化学信息学（ChemoPy），用于计算常用的结构和物理化学特征。它计算了16个药物特征组，由19个描述符组成，包括1135个描述符值。此外，它还提供了七种药物分子的分子指纹系统，包括拓扑指纹、电拓扑态（E-state）指纹、MACCS密钥、FP 4密钥、原子对指纹、拓扑扭转指纹和Morgan/循环指纹。通过应用半经验量子化学程序MOPAC，ChemoPy还可以方便地计算大量的3D分子描述符。
可用性
python包ChemoPy可以通过http：//code.google.com/p/pychem/downloads/list免费获得，它可以在Linux和MS-Windows上运行。
补充资料
补充数据可在Bioinformatics在线获得。
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.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.