protr-package: Protein Sequence Descriptor Calculation and Similarity Computation with R
Description
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: http://cbdd.csu.edu.cn:8080/protrweb/ .
The protr package is developed by Computational Biology and Drug Design
(CBDD) Group, Central South University.