nanxstats / Rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery
https://nanx.me/Rcpi/
Artistic License 2.0
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bioconductor bioinformatics cheminformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

Rcpi

bioc downloads R-CMD-check

Overview

Rcpi offers a molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery. For more information, please see our paper <DOI:10.1093/bioinformatics/btu624> (PDF).

Paper Citation

Formatted citation:

Dong-Sheng Cao, Nan Xiao, Qing-Song Xu, and Alex F. Chen. (2015). Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. Bioinformatics 31 (2), 279-281.

BibTeX entry:

@article{Rcpi2015,
  author  = {Cao, Dong-Sheng and Xiao, Nan and Xu, Qing-Song and Chen, Alex F.},
  title   = {{Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions}},
  journal = {Bioinformatics},
  year    = {2015},
  volume  = {31},
  number  = {2},
  pages   = {279--281},
  doi     = {10.1093/bioinformatics/btu624}
}

Browse the workflow and cheatsheet vignettes to get started.

Installation

Install Rcpi

Install the Rcpi package via BiocManager. If BiocManager is not already installed:

install.packages("BiocManager")

Then install Rcpi:

BiocManager::install("Rcpi")

Manage dependencies

Some features in the Rcpi package rely on certain R packages which may require specific system configurations to install from source. To make the build process robust, these dependencies have been configured as runtime dependencies. Here are some instructions for installing such dependencies to enable the features in Rcpi.

Install rcdk

rcdk can be installed from either CRAN or GitHub:

install.packages("rcdk", type = "source")
remotes::install_github("CDK-R/cdkr", subdir = "rcdk")

rcdk requires JDK and rJava to be installed and configured on your system. Check out the rJava readme for installation and troubleshooting instructions.

Install cheminformatics packages

Additional packages for cheminformatics capabilities are available from Bioconductor:

BiocManager::install(c("fmcsR", "ChemmineR", "ChemmineOB"))

ChemmineOB requires Open Babel to compile from source. Ensure Open Babel is properly installed on your system.

Features

Rcpi implemented and integrated the state-of-the-art protein sequence descriptors and molecular descriptors/fingerprints with R. For protein sequences, the Rcpi package could

For small molecules, the Rcpi package could

By combining various types of descriptors for drugs and proteins in different methods, interaction descriptors representing protein-protein or compound-protein interactions could be conveniently generated with Rcpi, including:

Several useful auxiliary utilities are also shipped with Rcpi:

The computed protein sequence descriptors, molecular descriptors/fingerprints, interaction descriptors and pairwise similarities are widely used in various research fields relevant to drug discovery, primarily bioinformatics, cheminformatics, proteochemometrics, and chemogenomics.

Contribute

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that the Rcpi project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.