Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions


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Documentation for package ‘BioMedR’ version 1.2.1

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A B C E G I M N O P R S T

BioMedR-package Toolkit for Compound-Protein Interaction in Drug Discovery

-- A --

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
apfp Frequent Atom Pairs
atomprop Standard atomic weights
Autocorrelation Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges

-- B --

bcl 2D descriptors of bcl2
BioMedR Toolkit for Compound-Protein Interaction in Drug Discovery
BMDrugMolCAS Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDNAGenBank Get DNA/RNA Sequences from Genbank by GI ID
BMgetDrug Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolChEMBL Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolDrugBank Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolKEGG Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolPubChem Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiChEMBL Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiDrugBank Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiKEGG Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiPubChem Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetProt Retrieve Protein Sequence in various Formats from Databases
BMgetProtFASTAKEGG Retrieve Protein Sequence in various Formats from Databases
BMgetProtFASTAUinProt Retrieve Protein Sequence in various Formats from Databases
BMgetProtPDBRCSBPDB Retrieve Protein Sequence in various Formats from Databases
BMgetProtSeqKEGG Retrieve Protein Sequence in various Formats from Databases
BMgetProtSeqRCSBPDB Retrieve Protein Sequence in various Formats from Databases
BMgetProtSeqUniProt Retrieve Protein Sequence in various Formats from Databases

-- C --

calcDrugFPSim Calculate Drug Molecule Similarity Derived by Molecular Fingerprints
calcParProtGOSim Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
calcParProtSeqSim Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment
calcTwoProtGOSim Protein Similarity Calculation based on Gene Ontology (GO) Similarity
calcTwoProtSeqSim Protein Sequence Alignment for Two Protein Sequences
checkDNA Check if the DNA sequence are in the 4 default types
checkProt Check if the protein sequence's amino acid types are the 20 default types
clusterCMP cluster compounds using a descriptor database
clusterJP Jarvis-Patrick Clustering
clusterMDS visualize clustering result using multi-dimensional scaling
clusterPlotSOMmap Plot self-organising map
clusterStat generate statistics on sizes of clusters
connectivity Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
Constitutional Calculates the Number of Amino Acids Descriptor
convAPtoFP Fingerprints from descriptor vectors
convSDFtoAP Atom pair library

-- E --

extrDNADAC The Dinucleotide-based Auto Covariance Descriptor
extrDNADACC The Dinucleotide-based Auto-cross Covariance Descriptor
extrDNADCC The Dinucleotide-based Cross Covariance Descriptor
extrDNAIncDiv The Increment Of Diversity Descriptors
extrDNAkmer The Basic Kmer Descriptor
extrDNAPseDNC The Pseudo Dinucleotide Composition Descriptor
extrDNAPseKNC The Pseudo K-tupler Composition Descriptor
extrDNATAC The Trinucleotide-based Auto Covariance Descriptor
extrDNATACC The Trinucleotide-based Auto-cross Covariance Descriptor
extrDNATCC The Trinucleotide-based Cross Covariance Descriptor
extrDrugAIO Calculates All the Molecular Descriptors in the BioMedR Package at Once
extrDrugALOGP Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugAminoAcidCount Calculates the Number of Amino Acids Descriptor
extrDrugAP Calculate the Atom Pair Fingerprints
extrDrugApol Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugAromaticAtomsCount Calculates the Number of Amino Acids Descriptor
extrDrugAromaticBondsCount Calculates the Number of Amino Acids Descriptor
extrDrugAtomCount Calculates the Number of Amino Acids Descriptor
extrDrugAutocorrelationcharge Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extrDrugAutocorrelationMass Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extrDrugAutocorrelationPolarizability Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extrDrugBCUT BCUT - Eigenvalue Based Descriptor
extrDrugBondCount Calculates the Number of Amino Acids Descriptor
extrDrugBPol Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugCarbonTypes Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugChiChain Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugChiCluster Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugChiPath Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugChiPathCluster Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugCPSA A Variety of Descriptors Combining Surface Area and Partial Charge Information
extrDrugECI Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugEstate Calculate the E-State Molecular Fingerprints (in Compact Format)
extrDrugEstateComplete Calculate the E-State Molecular Fingerprints (in Complete Format)
extrDrugExtended Calculate the Extended Molecular Fingerprints (in Compact Format)
extrDrugExtendedComplete Calculate the Extended Molecular Fingerprints (in Complete Format)
extrDrugFMF Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugFragmentComplexity Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugGraph Calculate the Graph Molecular Fingerprints (in Compact Format)
extrDrugGraphComplete Calculate the Graph Molecular Fingerprints (in Complete Format)
extrDrugGravitationalIndex Descriptor Characterizing the Mass Distribution of the Molecule.
extrDrugHBondAcceptorCount Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugHBondDonorCount Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugHybridization Calculate the Hybridization Molecular Fingerprints (in Compact Format)
extrDrugHybridizationComplete Calculate the Hybridization Molecular Fingerprints (in Complete Format)
extrDrugHybridizationRatio Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States
extrDrugIPMolecularLearning Calculates the Descriptor that Evaluates the Ionization Potential
extrDrugKappaShapeIndices Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices
extrDrugKierHallSmarts Descriptor that Counts the Number of Occurrences of the E-State Fragments
extrDrugKR Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)
extrDrugKRComplete Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)
extrDrugLargestChain Calculates the Number of Amino Acids Descriptor
extrDrugLargestPiSystem Calculates the Number of Amino Acids Descriptor
extrDrugLengthOverBreadth Descriptor Characterizing the Mass Distribution of the Molecule.
extrDrugLogP Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugLongestAliphaticChain Calculates the Number of Amino Acids Descriptor
extrDrugMACCS Calculate the MACCS Molecular Fingerprints (in Compact Format)
extrDrugMACCSComplete Calculate the MACCS Molecular Fingerprints (in Complete Format)
extrDrugMannholdLogP Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms
extrDrugMDE Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugMomentOfInertia Descriptor Characterizing the Mass Distribution of the Molecule.
extrDrugPetitjeanNumber Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugPetitjeanShapeIndex Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugPubChem Calculate the PubChem Molecular Fingerprints (in Compact Format)
extrDrugPubChemComplete Calculate the PubChem Molecular Fingerprints (in Complete Format)
extrDrugRotatableBondsCount Calculates the Number of Amino Acids Descriptor
extrDrugRuleOfFive Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugShortestPath Calculate the Shortest Path Molecular Fingerprints (in Compact Format)
extrDrugShortestPathComplete Calculate the Shortest Path Molecular Fingerprints (in Complete Format)
extrDrugStandard Calculate the Standard Molecular Fingerprints (in Compact Format)
extrDrugStandardComplete Calculate the Standard Molecular Fingerprints (in Complete Format)
extrDrugTPSA Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugVABC Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugVAdjMa Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugWeight Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugWeightedPath Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugWHIM Calculate Holistic Descriptors Described by Todeschini et al.
extrDrugWienerNumbers Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugZagrebIndex Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrPCMBLOSUM Generalized BLOSUM and PAM Matrix-Derived Descriptors
extrPCMDescScales Scales-Based Descriptors with 20+ classes of Molecular Descriptors
extrPCMFAScales Generalized Scales-Based Descriptors derived by Factor Analysis
extrPCMMDSScales Generalized Scales-Based Descriptors derived by Multidimensional Scaling
extrPCMPropScales Generalized AA-Properties Based Scales Descriptors
extrPCMScaleGap Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support)
extrPCMScales Generalized Scales-Based Descriptors derived by Principal Components Analysis
extrProtAAC Amino Acid Composition Descriptor
extrProtAPAAC Amphiphilic Pseudo Amino Acid Composition Descriptor
extrProtCTDC CTD Descriptors - Composition
extrProtCTDCClass CTD Descriptors - Composition (with Customized Amino Acid Classification Support)
extrProtCTDD CTD Descriptors - Distribution
extrProtCTDDClass CTD Descriptors - Distribution (with Customized Amino Acid Classification Support)
extrProtCTDT CTD Descriptors - Transition
extrProtCTDTClass CTD Descriptors - Transition (with Customized Amino Acid Classification Support)
extrProtCTriad Conjoint Triad Descriptor
extrProtCTriadClass Conjoint Triad Descriptor (with Customized Amino Acid Classification Support)
extrProtDC Dipeptide Composition Descriptor
extrProtFPGap Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support
extrProtGeary Geary Autocorrelation Descriptor
extrProtMoran Moran Autocorrelation Descriptor
extrProtMoreauBroto Normalized Moreau-Broto Autocorrelation Descriptor
extrProtPAAC Pseudo Amino Acid Composition Descriptor
extrProtPSSM Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence
extrProtPSSMAcc Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance
extrProtPSSMFeature Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)
extrProtQSO Quasi-Sequence-Order (QSO) Descriptor
extrProtSOCN Sequence-Order-Coupling Numbers
extrProtTC Tripeptide Composition Descriptor

-- G --

geometric Descriptor Characterizing the Mass Distribution of the Molecule.
getCCI Generating Interaction Descriptors
getCDI Generating Interaction Descriptors
getCPI Generating Interaction Descriptors
getDDI Generating Interaction Descriptors
getDPI Generating Interaction Descriptors
getDrug Retrieve Drug Molecules in MOL and SMILES Format from Databases
getPPI Generating Interaction Descriptors
getProt Retrieve Protein Sequence in various Formats from Databases

-- I --

IncDiv The Increment Of Diversity Descriptors

-- M --

make_kmer_index Calculate The Basic Kmer Feature Vector

-- N --

NNeighbors Nearest Neighbors

-- O --

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

-- P --

parGOSim Protein/DNA Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
parSeqSim Parallellized Protein/DVA Sequence Similarity Calculation based on Sequence Alignment
plotStructure Plots compound structure(s) for molecules stored in SDF and SDFset containers
pls.cv The Cross-Validation of Classification and Regression models using Partial Least Squares
property Calculates Atom Additive logP and Molar Refractivity Values Descriptor

-- R --

readFASTA Read Protein/DNA Sequences in FASTA Format
readMolFromSDF Read Molecules from SDF Files and Return Parsed Java Molecular Object
readMolFromSmi Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List
readPDB Read Protein Sequences in PDB Format
revchars The Reverse chars
rf.cv The Cross-Validation of Classification and Regression models using Random Forest
rf.fs Random Forest Cross-Valdidation for feature selection

-- S --

sdfbcl SD file in 'SDFset' object
searchDrug Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search
segProt Protein Sequence Segmentation
som.bcl kohonen object

-- T --

topology Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
twoGOSim Protein/DNA Similarity Calculation based on Gene Ontology (GO) Similarity
twoSeqSim Protein/DNA Sequence Alignment for Two Protein Sequences