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Rcpi specifications

Information


Unique identifier OMICS_07112
Name Rcpi
Alternative name Compound-Protein Interaction with R
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.16.2
Stability Stable
Requirements
methods, stats, BiocGenerics, utils, Biostrings, RUnit, rmarkdown, knitr, foreach, RCurl, GOSemSim, rjson, doParallel, R(>=3.0.2), ChemmineR, fmcsR, rcdk(>=3.3.8)
Maintained Yes

Versioning


No version available

Documentation


Publication for Compound-Protein Interaction with R

Rcpi citations

 (4)
library_books

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

2018
J Cheminform
PMCID: 5861255
PMID: 29556758
DOI: 10.1186/s13321-018-0270-2

[…] ], CDK [], rcdk, PaDEL [], Cinfony [], Chemopy [], ChemDes [], BioJava [], BioTriangle [], bioclipse [], propy [], PyDPI [], Biopython, repDNA [], CDK-Taverna [], protr/protrWeb [], ChemmineR [], and Rcpi [] have been established to calculate such descriptors. However, currently available solutions are often limited to certain types of descriptors, lack flexibility, and usually difficult to seamle […]

library_books

Mordred: a molecular descriptor calculator

2018
J Cheminform
PMCID: 5801138
PMID: 29411163
DOI: 10.1186/s13321-018-0258-y

[…] orts Python 2.Furthermore, PyDPI can calculate small molecule descriptors as well as protein descriptors. However, it has advantages and limitations that are similar to those of ChemoPy. In addition, Rcpi (the protein and small molecule descriptor calculation package for R []) is the only R package to calculate small molecular descriptors and protein descriptors. It can calculate only 307 small mo […]

library_books

Drug target interaction prediction via class imbalance aware ensemble learning

2016
BMC Bioinformatics
PMCID: 5259867
PMID: 28155697
DOI: 10.1186/s12859-016-1377-y

[…] After having obtained the interaction data, we generated features for the drugs and targets respectively. Particularly, descriptors for drugs were calculated using the Rcpi [] package. Examples of drug features include constitutional, topological and geometrical descriptors among other molecular properties. Note that biotech drugs have been excluded from this study […]

library_books

Origin of aromatase inhibitory activity via proteochemometric modeling

2016
PeerJ
PMCID: 4868594
PMID: 27190705
DOI: 10.7717/peerj.1979

[…] udy, cross-terms were calculated as the mathematical product of the compounds descriptors with those of the protein descriptors. Cross-terms were computed using the getCPI function from the R package Rcpi (). Moreover, the total number of cross-terms computed for self interaction (i.e., compound × compound and protein × protein) was obtained as follows: (1)NN−12where N is the total number of descr […]

Citations

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Rcpi institution(s)
School of Pharmaceutical Sciences and School of Mathematics and Statistics, Central South University, Changsha, China

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