protr: Protein Sequence Descriptor Calculation and Similarity Computation with R

The protr package focus on offering a unique and comprehensive toolkit for protein sequence descriptor calculation and similarity computation. The descriptors included in the protr package are extensively utilized in Bioinformatics and Chemogenomics research. The qualitative descriptors listed in protr include Amino Acid Composition (Amino Acid Composition/Dipeptide Composition/Tripeptide Composition) descriptor, Autocorrelation (Normalized Moreau-Broto Autocorrelation/Moran Autocorrelation/Geary Autocorrelation) descriptor, CTD (Composition/Transition/Distribution) descriptor, Conjoint Traid descriptor, Quasi-sequence Order (Sequence Order Coupling Number/Quasi-sequence Order Descriptors) descriptor and Pseudo Amino Acid Composition (Pseudo Amino Acid Composition/Amphiphilic Pseudo Amino Acid Composition) descriptor. The quantitative descriptors, for Proteochemometric (PCM) Modeling, includes the Generalized Scales-Based Descriptors derived by Principal Components Analysis, Generalized Scales-Based Descriptors derived by AA-Properties (AAindex), Generalized Scales-Based Descriptors derived by 20+ classes of 2D and 3D Molecular Descriptors (Topological, WHIM, VHSE, etc.), Generalized Scales-Based Descriptors derived by Factor Analysis, Generalized Scales-Based Descriptors derived by Multidimensional Scaling, and Generalized BLOSUM/PAM Matrix-Derived Descriptors. The protr package also integrates the functionality of parallellized similarity computation derived by protein sequence alignment and Gene Ontology (GO) semantic similarity measures between a list of protein sequences / GO terms / Entrez Gene IDs. ProtrWeb, the web service built on protr, is located at: . The protr package is developed by Computational Biology and Drug Design (CBDD) Group, Central South University.

Version: 0.3-1
Suggests: Biostrings, GOSemSim, foreach, doParallel
Published: 2014-08-24
Author: Nan Xiao, Qingsong Xu, Dongsheng Cao
Maintainer: Nan Xiao <road2stat at>
License: BSD 3-clause License + file LICENSE
NeedsCompilation: no
Citation: protr citation info
Materials: README NEWS
CRAN checks: protr results


Reference manual: protr.pdf
Vignettes: protr: Protein Sequence-Derived Structural and Physiochemical Descriptors Calculation with R
Package source: protr_0.3-1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X Snow Leopard binaries: r-release: protr_0.3-1.tgz, r-oldrel: protr_0.3-1.tgz
OS X Mavericks binaries: r-release: protr_0.3-1.tgz
Old sources: protr archive