Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions
Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions
复制标题
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
DOI：
10.1093/bioinformatics/btu624
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发表时间：
2015-01-15
期刊：
影响因子：
5.8
通讯作者：
Chen, Alex F.
中科院分区：
文献类型：
--
作者：
Cao, Dong-Sheng;Xiao, Nan;Chen, Alex F.
未标记
在化学信息学和生物信息学领域，各种预测建模的主要计算挑战之一是找到合适的方法来有效地表示所研究的分子，例如小分子，蛋白质甚至复杂的相互作用。为了解决这个问题，我们开发了一个免费的R/Bioconductor软件包，称为化合物-蛋白质相互作用与R（Rcpi），用于药物，蛋白质和更复杂的相互作用的复杂分子表示，包括蛋白质-蛋白质和化合物-蛋白质相互作用。Rcpi可以从氨基酸序列中计算蛋白质和多肽的大量结构和物理化学特征，从拓扑结构和蛋白质相互作用中计算小分子的分子描述符，以及化合物与蛋白质相互作用的描述符。除了主要功能外，Rcpi还可以提供一些有用的辅助工具，以方便用户的需要。使用该软件包计算的描述符，用户可以方便地应用R中的各种统计机器学习方法来解决计算生物学和药物发现中的各种生物和药物研究问题。
可用性和执行
Rcpi可从Bioconductor网站（http：//bioconductor.org/packages/release/bioc/html/Rcpi.html）免费获得。
UNLABELLED
In chemoinformatics and bioinformatics fields, one of the main computational challenges in various predictive modeling is to find a suitable way to effectively represent the molecules under investigation, such as small molecules, proteins and even complex interactions. To solve this problem, we developed a freely available R/Bioconductor package, called Compound-Protein Interaction with R (Rcpi), for complex molecular representation from drugs, proteins and more complex interactions, including protein-protein and compound-protein interactions. Rcpi could calculate a large number of structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of small molecules from their topology and protein-protein interaction and compound-protein interaction descriptors. In addition to main functionalities, Rcpi could also provide a number of useful auxiliary utilities to facilitate the user's need. With the descriptors calculated by this package, the users could conveniently apply various statistical machine learning methods in R to solve various biological and drug research questions in computational biology and drug discovery.
AVAILABILITY AND IMPLEMENTATION
Rcpi is freely available from the Bioconductor site (http://bioconductor.org/packages/release/bioc/html/Rcpi.html).