Protein/Peptide Sequence Descriptors

Functions for calculating protein/peptide sequence descirptors.

extractAAC()

Amino Acid Composition Descriptor

extractDC()

Dipeptide Composition Descriptor

extractTC()

Tripeptide Composition Descriptor

extractMoreauBroto()

Normalized Moreau-Broto Autocorrelation Descriptor

extractMoran()

Moran Autocorrelation Descriptor

extractGeary()

Geary Autocorrelation Descriptor

extractCTDC()

CTD Descriptors - Composition

extractCTDCClass()

CTD Descriptors - Composition (with customized amino acid classification support)

extractCTDDClass()

CTD Descriptors - Distribution (with customized amino acid classification support)

extractCTDTClass()

CTD Descriptors - Transition (with customized amino acid classification support)

extractCTDT()

CTD Descriptors - Transition

extractCTDD()

CTD Descriptors - Distribution

extractCTriad()

Conjoint Triad Descriptor

extractCTriadClass()

Conjoint Triad Descriptor (with customized amino acid classification support)

extractSOCN()

Sequence-Order-Coupling Numbers

extractQSO()

Quasi-Sequence-Order (QSO) Descriptor

extractPAAC()

Pseudo Amino Acid Composition (PseAAC) Descriptor

extractAPAAC()

Amphiphilic Pseudo Amino Acid Composition (APseAAC) Descriptor

Profile-Based Protein/Peptide Sequence Descriptors

Functions for calculating the profile-based (PSSM) descirptors.

extractPSSM()

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

extractPSSMAcc()

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

extractPSSMFeature()

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

acc()

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

Proteochemometric Modeling (PCM) Descriptors

Functions for calculating proteochemometric modeling (PCM) descriptors.

extractScales()

Scales-Based Descriptors derived by Principal Components Analysis

extractScalesGap()

Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support)

extractProtFP()

Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)

extractProtFPGap()

Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support

extractDescScales()

Scales-Based Descriptors with 20+ classes of Molecular Descriptors

extractFAScales()

Scales-Based Descriptors derived by Factor Analysis

extractMDSScales()

Scales-Based Descriptors derived by Multidimensional Scaling

extractBLOSUM()

BLOSUM and PAM Matrix-Derived Descriptors

Similarity Measures between Proteins

Functions for calculating protein sequence alignment based similarity measures and GO-based semantic similarity measures.

parSeqSim()

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment (In-Memory Version)

parSeqSimDisk()

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment (Disk-Based Version)

twoSeqSim()

Protein Sequence Alignment for Two Protein Sequences

parGOSim()

Protein Similarity Calculation based on Gene Ontology (GO) Similarity

twoGOSim()

Protein Similarity Calculation based on Gene Ontology (GO) Similarity

Helper Functions for Pre-Processing Protein Sequences

Functions for pre-processing protein sequences.

getUniProt()

Retrieve Protein Sequences from UniProt by Protein ID

readFASTA()

Read Protein Sequences in FASTA Format

readPDB()

Read Protein Sequences in PDB Format

protcheck()

Protein sequence amino acid type sanity check

protseg()

Protein Sequence Segmentation/Partition

removeGaps()

Remove or replace gaps from protein sequences.

protr-package

protr: Generating Various Numerical Representation Schemes for Protein Sequences

Precomputed Molecular Descriptors for the 20 Amino Acids

Precomputed molecular descriptors for the 20 amino acids.

AAindex

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

AAMetaInfo

Meta Information for the 20 Amino Acids

OptAA3d

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

AA2DACOR

2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon

AA3DMoRSE

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

AAACF

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

AABurden

Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon

AAConn

Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon

AAConst

Constitutional Descriptors for 20 Amino Acids calculated by Dragon

AACPSA

CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio

AADescAll

All 2D Descriptors for 20 Amino Acids calculated by Dragon

AAEdgeAdj

Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon

AAEigIdx

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

AAFGC

Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon

AAGeom

Geometrical Descriptors for 20 Amino Acids calculated by Dragon

AAGETAWAY

GETAWAY Descriptors for 20 Amino Acids calculated by Dragon

AAInfo

Information Indices Descriptors for 20 Amino Acids calculated by Dragon

AAMOE2D

2D Descriptors for 20 Amino Acids calculated by MOE 2011.10

AAMOE3D

3D Descriptors for 20 Amino Acids calculated by MOE 2011.10

AAMolProp

Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon

AARandic

Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon

AARDF

RDF Descriptors for 20 Amino Acids calculated by Dragon

AATopo

Topological Descriptors for 20 Amino Acids calculated by Dragon

AATopoChg

Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon

AAWalk

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

AAWHIM

WHIM Descriptors for 20 Amino Acids calculated by Dragon

BLOSUM and PAM matrices for the 20 Amino Acids

BLOSUM and PAM matrices for the 20 amino acids.

AABLOSUM45

BLOSUM45 Matrix for 20 Amino Acids

AABLOSUM50

BLOSUM50 Matrix for 20 Amino Acids

AABLOSUM62

BLOSUM62 Matrix for 20 Amino Acids

AABLOSUM80

BLOSUM80 Matrix for 20 Amino Acids

AABLOSUM100

BLOSUM100 Matrix for 20 Amino Acids

AAPAM30

PAM30 Matrix for 20 Amino Acids

AAPAM40

PAM40 Matrix for 20 Amino Acids

AAPAM70

PAM70 Matrix for 20 Amino Acids

AAPAM120

PAM120 Matrix for 20 Amino Acids

AAPAM250

PAM250 Matrix for 20 Amino Acids