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"AAMOE3D", "title": "3D Descriptors for 20 Amino Acids calculated by MOE 2011.10", "topics": [ "AAMOE3D" ] }, { "page": "AAMolProp", "title": "Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAMolProp" ] }, { "page": "AAPAM120", "title": "PAM120 Matrix for 20 Amino Acids", "topics": [ "AAPAM120" ] }, { "page": "AAPAM250", "title": "PAM250 Matrix for 20 Amino Acids", "topics": [ "AAPAM250" ] }, { "page": "AAPAM30", "title": "PAM30 Matrix for 20 Amino Acids", "topics": [ "AAPAM30" ] }, { "page": "AAPAM40", "title": "PAM40 Matrix for 20 Amino Acids", "topics": [ "AAPAM40" ] }, { "page": "AAPAM70", "title": "PAM70 Matrix for 20 Amino Acids", "topics": [ "AAPAM70" ] }, { "page": "AARandic", "title": "Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AARandic" ] }, { "page": "AARDF", "title": "RDF Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AARDF" ] }, { "page": "AATopo", "title": "Topological Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AATopo" ] }, { "page": "AATopoChg", "title": "Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AATopoChg" ] }, { "page": "AAWalk", "title": "Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAWalk" ] }, { "page": "AAWHIM", "title": "WHIM Descriptors for 20 Amino Acids calculated by Dragon", "topics": [ "AAWHIM" ] }, { "page": "ACC", "title": "Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length", "topics": [ "acc" ] }, { "page": "crossSetSim", "title": "Parallel Protein Sequence Similarity Calculation Between Two Sets Based on Sequence Alignment (In-Memory Version)", "topics": [ "crossSetSim" ] }, { "page": "crossSetSimDisk", "title": "Parallel Protein Sequence Similarity Calculation Between Two Sets Based on Sequence Alignment (Disk-Based Version)", "topics": [ "crossSetSimDisk" ] }, { "page": "extractAAC", "title": "Amino Acid Composition Descriptor", "topics": [ "extractAAC" ] }, { "page": "extractAPAAC", "title": "Amphiphilic Pseudo Amino Acid Composition (APseAAC) Descriptor", "topics": [ "extractAPAAC" ] }, { "page": "extractBLOSUM", "title": "BLOSUM and PAM Matrix-Derived Descriptors", "topics": [ "extractBLOSUM" ] }, { "page": "extractCTDC", "title": "CTD Descriptors - Composition", "topics": [ "extractCTDC" ] }, { "page": "extractCTDCClass", "title": "CTD Descriptors - Composition (with customized amino acid classification support)", "topics": [ "extractCTDCClass" ] }, { "page": "extractCTDD", "title": "CTD Descriptors - Distribution", "topics": [ "extractCTDD" ] }, { "page": "extractCTDDClass", "title": "CTD Descriptors - Distribution (with customized amino acid classification support)", "topics": [ "extractCTDDClass" ] }, { "page": "extractCTDT", "title": "CTD Descriptors - Transition", "topics": [ "extractCTDT" ] }, { "page": "extractCTDTClass", "title": "CTD Descriptors - Transition (with customized amino acid classification support)", "topics": [ "extractCTDTClass" ] }, { "page": "extractCTriad", "title": "Conjoint Triad Descriptor", "topics": [ "extractCTriad" ] }, { "page": "extractCTriadClass", "title": "Conjoint Triad Descriptor (with customized amino acid classification support)", "topics": [ "extractCTriadClass" ] }, { "page": "extractDC", "title": "Dipeptide Composition Descriptor", "topics": [ "extractDC" ] }, { "page": "extractDescScales", "title": "Scales-Based Descriptors with 20+ classes of Molecular Descriptors", "topics": [ "extractDescScales" ] }, { "page": "extractFAScales", "title": "Scales-Based Descriptors derived by Factor Analysis", "topics": [ "extractFAScales" ] }, { "page": "extractGeary", "title": "Geary Autocorrelation Descriptor", "topics": [ "extractGeary" ] }, { "page": "extractMDSScales", "title": "Scales-Based Descriptors derived by Multidimensional Scaling", "topics": [ "extractMDSScales" ] }, { "page": "extractMoran", "title": "Moran Autocorrelation Descriptor", "topics": [ "extractMoran" ] }, { "page": "extractMoreauBroto", "title": "Normalized Moreau-Broto Autocorrelation Descriptor", "topics": [ "extractMoreauBroto" ] }, { "page": "extractPAAC", "title": "Pseudo Amino Acid Composition (PseAAC) Descriptor", "topics": [ "extractPAAC" ] }, { "page": "extractProtFP", "title": "Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)", "topics": [ "extractProtFP" ] }, { "page": "extractProtFPGap", "title": "Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support", "topics": [ "extractProtFPGap" ] }, { "page": "extractPSSM", "title": "Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence", "topics": [ "extractPSSM" ] }, { "page": "extractPSSMAcc", "title": "Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance", "topics": [ "extractPSSMAcc" ] }, { "page": "extractPSSMFeature", "title": "Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)", "topics": [ "extractPSSMFeature" ] }, { "page": "extractQSO", "title": "Quasi-Sequence-Order (QSO) Descriptor", "topics": [ "extractQSO" ] }, { "page": "extractScales", "title": "Scales-Based Descriptors derived by Principal Components Analysis", "topics": [ "extractScales" ] }, { "page": "extractScalesGap", "title": "Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support)", "topics": [ "extractScalesGap" ] }, { "page": "extractSOCN", "title": "Sequence-Order-Coupling Numbers", "topics": [ "extractSOCN" ] }, { "page": "extractTC", "title": "Tripeptide Composition Descriptor", "topics": [ "extractTC" ] }, { "page": "getUniProt", "title": "Retrieve Protein Sequences from UniProt by Protein ID", "topics": [ "getUniProt" ] }, { "page": "OptAA3d", "title": "OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)", "topics": [ "OptAA3d" ] }, { "page": "parGOSim", "title": "Protein Similarity Calculation based on Gene Ontology (GO) Similarity", "topics": [ "parGOSim" ] }, { "page": "parSeqSim", "title": "Parallel Protein Sequence Similarity Calculation Based on Sequence Alignment (In-Memory Version)", "topics": [ "parSeqSim" ] }, { "page": "parSeqSimDisk", "title": "Parallel Protein Sequence Similarity Calculation Based on Sequence Alignment (Disk-Based Version)", "topics": [ "parSeqSimDisk" ] }, { "page": "protcheck", "title": "Protein sequence amino acid type sanity check", "topics": [ "protcheck" ] }, { "page": "protseg", "title": "Protein Sequence Segmentation/Partition", "topics": [ "protseg" ] }, { "page": "readFASTA", "title": "Read Protein Sequences in FASTA Format", "topics": [ "readFASTA" ] }, { "page": "readPDB", "title": "Read Protein Sequences in PDB Format", "topics": [ "readPDB" ] }, { "page": "removeGaps", "title": "Remove or replace gaps from protein sequences.", "topics": [ "removeGaps" ] }, { "page": "twoGOSim", "title": "Protein Similarity Calculation based on Gene Ontology (GO) Similarity", "topics": [ "twoGOSim" ] }, { "page": "twoSeqSim", "title": "Protein Sequence Alignment for Two Protein Sequences", "topics": [ "twoSeqSim" ] } ], "_pkglogo": "https://github.com/nanxstats/protr/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/nanxstats/protr/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "protr.Rmd", "filename": "protr.html", "title": "protr: R package for generating various numerical representation schemes of protein sequences", "author": "Nan Xiao ", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "An example predictive modeling workflow", "Package overview", "Commonly used descriptors", "Amino acid composition descriptor", "Dipeptide composition descriptor", "Tripeptide composition descriptor", "Autocorrelation descriptors", "Normalized Moreau-Broto autocorrelation descriptors", "Moran autocorrelation 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