Learn R Programming

⚠️There's a newer version (1.7-5) of this package.Take me there.

protr (version 0.4-1)

Generating Various Numerical Representation Schemes of Protein Sequence

Description

Comprehensive toolkit for generating various numerical representation schemes of protein sequence. The descriptors and similarity scores included are extensively utilized in bioinformatics and chemogenomics research.

Copy Link

Version

Install

install.packages('protr')

Monthly Downloads

581

Version

0.4-1

License

BSD 3-clause License + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/road2stat/protr

Maintainer

Nan Xiao

Last Published

October 10th, 2014

Functions in protr (0.4-1)

Constitutional Descriptors for 20 Amino Acids calculated by Dragon

extractFAScales

Generalized Scales-Based Descriptors derived by Factor Analysis

PAM30 Matrix for 20 Amino Acids

extractDescScales

Scales-Based Descriptors with 20+ classes of Molecular Descriptors

PAM250 Matrix for 20 Amino Acids

Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon

Get Protein Sequences from UniProt by Protein ID

Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon

BLOSUM100 Matrix for 20 Amino Acids

BLOSUM45 Matrix for 20 Amino Acids

3D Descriptors for 20 Amino Acids calculated by MOE 2011.10

Generalized BLOSUM and PAM Matrix-Derived Descriptors

extractMDSScales

Generalized Scales-Based Descriptors derived by Multidimensional Scaling

Protein Sequence Segmentation

PAM70 Matrix for 20 Amino Acids

Information Indices Descriptors for 20 Amino Acids calculated by Dragon

2D Descriptors for 20 Amino Acids calculated by MOE 2011.10

Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence

3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon

Quasi-Sequence-Order (QSO) Descriptor

Conjoint Triad Descriptor

Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance

Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon

Geometrical Descriptors for 20 Amino Acids calculated by Dragon

CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio

Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon

AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids

Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon

Sequence-Order-Coupling Numbers

PAM40 Matrix for 20 Amino Acids

GETAWAY Descriptors for 20 Amino Acids calculated by Dragon

Tripeptide Composition Descriptor

BLOSUM80 Matrix for 20 Amino Acids

Read Protein Sequences in PDB Format

Read Protein Sequences in FASTA Format

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment

BLOSUM62 Matrix for 20 Amino Acids

2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon

CTD Descriptors - Transition

Topological Descriptors for 20 Amino Acids calculated by Dragon

Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity

RDF Descriptors for 20 Amino Acids calculated by Dragon

extractPropScales

Generalized AA-Properties Based Scales Descriptors

Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length

CTD Descriptors - Distribution

Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon

PAM120 Matrix for 20 Amino Acids

WHIM Descriptors for 20 Amino Acids calculated by Dragon

Meta Information for the 20 Amino Acids

All 2D Descriptors for 20 Amino Acids calculated by Dragon

BLOSUM50 Matrix for 20 Amino Acids

Dipeptide Composition Descriptor

Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon

extractMoreauBroto

Normalized Moreau-Broto Autocorrelation Descriptor

Check if the protein sequence's amino acid types are in the 20 default types

Amino Acid Composition Descriptor

Amphiphilic Pseudo Amino Acid Composition Descriptor

Pseudo Amino Acid Composition Descriptor

OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)

extractPSSMFeature

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

Generating Various Numerical Representation Schemes of Protein Sequence

Protein Sequence Alignment for Two Protein Sequences

Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon

Geary Autocorrelation Descriptor

Moran Autocorrelation Descriptor

Generalized Scales-Based Descriptors derived by Principal Components Analysis

Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon

CTD Descriptors - Composition

Protein Similarity Calculation based on Gene Ontology (GO) Similarity