PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.
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PyBioMed：一个 Python 库，用于化学物质、蛋白质和 DNA 的各种分子表示及其相互作用
DOI：
10.1186/s13321-018-0270-2
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发表时间：
2018-03-20
影响因子：
8.6
通讯作者：
Cao DS
中科院分区：
文献类型：
--
作者：
Dong J;Yao ZJ;Zhang L;Luo F;Lin Q;Lu AP;Chen AF;Cao DS
With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important. So far, there are no suitable toolkits that can effectively link the chemical and biological space in view of molecular representation. To further explore these complex data, an integrated toolkit for various molecular representation is urgently needed which could be easily integrated with data mining algorithms to start a full data analysis pipeline. Herein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions. PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. The current version of PyBioMed could calculate 775 chemical descriptors and 19 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA descriptors from nucleotide sequences, and interaction descriptors from pairwise samples using three different combining strategies. Several examples and five real-life applications were provided to clearly guide the users how to use PyBioMed as an integral part of data analysis projects. By using PyBioMed, users are able to start a full pipelining from getting molecular data, pretreating molecules, molecular representation to constructing machine learning models conveniently. PyBioMed provides various user-friendly and highly customized APIs to calculate various features of biological molecules and complex interaction samples conveniently, which aims at building integrated analysis pipelines from data acquisition, data checking, and descriptor calculation to modeling. PyBioMed is freely available at http://projects.scbdd.com/pybiomed.html.
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影响因子：
14.8
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
使用基于核的方法探索化学数据中的非线性关系
DOI：
10.1016/j.chemolab.2011.02.004
发表时间：
2011-05-01
影响因子：
3.9
作者：
Cao, Dong-Sheng;Liang, Yi-Zeng;Fu, Guang-Hui
通讯作者：
Fu, Guang-Hui
Rcpi：R/Bioconductor 包，用于生成蛋白质、化合物及其相互作用的各种描述符
影响因子：
5.8
作者：
Cao, Dong-Sheng;Xiao, Nan;Chen, Alex F.
通讯作者：
Chen, Alex F.
DOI：
10.1073/pnas.92.19.8700
发表时间：
1995-09-12
影响因子：
11.1
作者：
DUBCHAK, I;MUCHNIK, I;KIM, SH
通讯作者：
KIM, SH
影响因子：
8.6
作者：
Cortes-Ciriano I;van Westen GJ;Lenselink EB;Murrell DS;Bender A;Malliavin T
通讯作者：
Malliavin T