Protein Sequence Descriptor Calculation and Similarity Computation with R


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Documentation for package ‘protr’ version 0.2-1

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protr-package Protein Sequence Descriptor Calculation and Similarity Computation with R
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 Descriptor
extractBLOSUM Generalized BLOSUM and PAM Matrix-Derived Descriptors
extractCTDC CTD Descriptors - Composition
extractCTDD CTD Descriptors - Distribution
extractCTDT CTD Descriptors - Transition
extractCTriad Conjoint Triad Descriptor
extractDC Dipeptide Composition Descriptor
extractDescScales Scales-Based Descriptors with 20+ classes of Molecular Descriptors
extractFAScales Generalized Scales-Based Descriptors derived by Factor Analysis
extractGeary Geary Autocorrelation Descriptor
extractMDSScales Generalized Scales-Based Descriptors derived by Multidimensional Scaling
extractMoran Moran Autocorrelation Descriptor
extractMoreauBroto Normalized Moreau-Broto Autocorrelation Descriptor
extractPAAC Pseudo Amino Acid Composition Descriptor
extractPropScales Generalized AA-Properties Based Scales Descriptors
extractQSO Quasi-Sequence-Order (QSO) Descriptor
extractScales Generalized Scales-Based Descriptors derived by Principal Components Analysis
extractSOCN Sequence-Order-Coupling Numbers
extractTC Tripeptide Composition Descriptor
getUniProt Get Protein Sequences from UniProt by Protein ID
OptAA3d OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)
parGOSim Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
parSeqSim Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment
protcheck Check if the protein sequence's amino acid types are in the 20 default types
protr Protein Sequence Descriptor Calculation and Similarity Computation with R
protseg Protein Sequence Segmentation
readFASTA Read Protein Sequences in FASTA Format
readPDB Read Protein Sequences in PDB Format
twoGOSim Protein Similarity Calculation based on Gene Ontology (GO) Similarity
twoSeqSim Protein Sequence Alignment for Two Protein Sequences