Package index • protr

Protein sequence descriptors

Calculate protein and peptide sequence descriptors.

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

PSSM descriptors

Calculate PSSM (profile-based) protein and peptide sequence descriptors.

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

PCM descriptors

Calculate PCM (proteochemometric modeling) 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

Calculate protein sequence alignment based similarity measures and GO-based semantic similarity measures.

parSeqSim(): Parallel Protein Sequence Similarity Calculation Based on Sequence Alignment (In-Memory Version)

parSeqSimDisk(): Parallel Protein Sequence Similarity Calculation Based on Sequence Alignment (Disk-Based Version)

crossSetSim(): Parallel Protein Sequence Similarity Calculation Between Two Sets Based on Sequence Alignment (In-Memory Version)

crossSetSimDisk(): Parallel Protein Sequence Similarity Calculation Between Two Sets 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

Pre-process protein sequences

Helper 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 protr-package: protr: Generating Various Numerical Representation Schemes for Protein Sequences

Precomputed molecular descriptors

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

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