title: Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.
abstract: 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.
  
  
  METHODS
  Rcpi is freely available from the Bioconductor site (http://bioconductor.org/packages/release/bioc/html/Rcpi.html).
authors.affiliation: School of Pharmaceutical Sciences and School of Mathematics and Statistics, Central South University, Changsha 410083, P. R. China.
authors.forename: Dong-Sheng
authors.initials: DS
authors.lastname: Cao
authors.affiliation: School of Pharmaceutical Sciences and School of Mathematics and Statistics, Central South University, Changsha 410083, P. R. China.
authors.forename: Nan
authors.initials: N
authors.lastname: Xiao
authors.affiliation: School of Pharmaceutical Sciences and School of Mathematics and Statistics, Central South University, Changsha 410083, P. R. China.
authors.forename: Qing-Song
authors.initials: QS
authors.lastname: Xu
authors.affiliation: School of Pharmaceutical Sciences and School of Mathematics and Statistics, Central South University, Changsha 410083, P. R. China.
authors.forename: Alex F
authors.initials: AF
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D062313:Databases, Pharmaceutical; D055808:Drug Discovery; D015507:Drugs, Investigational / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software
chemical_list: D015507:Drugs, Investigational; D011506:Proteins