# Generating Various Numerical Representation Schemes for Protein Sequences

## Documentation for package ‘protr’ version 1.6-2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
AABLOSUM100 | BLOSUM100 Matrix for 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
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
AAindex | AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids
AAInfo | Information Indices Descriptors for 20 Amino Acids calculated by Dragon
AAMetaInfo | Meta Information for the 20 Amino Acids
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
AAPAM120 | PAM120 Matrix for 20 Amino Acids
AAPAM250 | PAM250 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
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
acc | Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length
extractAAC | Amino Acid Composition Descriptor
extractAPAAC | Amphiphilic Pseudo Amino Acid Composition (APseAAC) Descriptor
extractBLOSUM | BLOSUM and PAM Matrix-Derived Descriptors
extractCTDC | CTD Descriptors - Composition
extractCTDCClass | CTD Descriptors - Composition (with customized amino acid classification support)
extractCTDD | CTD Descriptors - Distribution
extractCTDDClass | CTD Descriptors - Distribution (with customized amino acid classification support)
extractCTDT | CTD Descriptors - Transition
extractCTDTClass | CTD Descriptors - Transition (with customized amino acid classification support)
extractCTriad | Conjoint Triad Descriptor
extractCTriadClass | Conjoint Triad Descriptor (with customized amino acid classification support)
extractDC | Dipeptide Composition Descriptor
extractDescScales | Scales-Based Descriptors with 20+ classes of Molecular Descriptors
extractFAScales | Scales-Based Descriptors derived by Factor Analysis
extractGeary | Geary Autocorrelation Descriptor
extractMDSScales | Scales-Based Descriptors derived by Multidimensional Scaling
extractMoran | Moran Autocorrelation Descriptor
extractMoreauBroto | Normalized Moreau-Broto Autocorrelation Descriptor
extractPAAC | Pseudo Amino Acid Composition (PseAAC) Descriptor
extractProtFP | Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)
extractProtFPGap | Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support
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)
extractQSO | Quasi-Sequence-Order (QSO) Descriptor
extractScales | Scales-Based Descriptors derived by Principal Components Analysis
extractScalesGap | Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support)
extractSOCN | Sequence-Order-Coupling Numbers
extractTC | Tripeptide Composition Descriptor
getUniProt | Retrieve Protein Sequences from UniProt by Protein ID
OptAA3d | OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)
parGOSim | Protein Similarity Calculation based on Gene Ontology (GO) Similarity
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)
protcheck | Protein sequence amino acid type sanity check
protseg | Protein Sequence Segmentation/Partition
readFASTA | Read Protein Sequences in FASTA Format
readPDB | Read Protein Sequences in PDB Format
removeGaps | Remove or replace gaps from protein sequences.
twoGOSim | Protein Similarity Calculation based on Gene Ontology (GO) Similarity
twoSeqSim | Protein Sequence Alignment for Two Protein Sequences