Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery


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Documentation for package ‘Rcpi’ version 1.40.1

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A C E G O R S

-- 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

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calcDrugFPSim Calculate Drug Molecule Similarity Derived by Molecular Fingerprints
calcDrugMCSSim Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search
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
checkProt Check if the protein sequence's amino acid types are the 20 default types
convMolFormat Chemical File Formats Conversion

-- E --

extractDrugAIO Calculate All Molecular Descriptors in Rcpi at Once
extractDrugALOGP Calculate Atom Additive logP and Molar Refractivity Values Descriptor
extractDrugAminoAcidCount Calculate the Number of Amino Acids Descriptor
extractDrugApol Calculate the Sum of the Atomic Polarizabilities Descriptor
extractDrugAromaticAtomsCount Calculate the Number of Aromatic Atoms Descriptor
extractDrugAromaticBondsCount Calculate the Number of Aromatic Bonds Descriptor
extractDrugAtomCount Calculate the Number of Atom Descriptor
extractDrugAutocorrelationCharge Calculate the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extractDrugAutocorrelationMass Calculate the Moreau-Broto Autocorrelation Descriptors using Atomic Weight
extractDrugAutocorrelationPolarizability Calculate the Moreau-Broto Autocorrelation Descriptors using Polarizability
extractDrugBCUT BCUT - Eigenvalue Based Descriptor
extractDrugBondCount Calculate the Descriptor Based on the Number of Bonds of a Certain Bond Order
extractDrugBPol Calculate the Descriptor that Describes the Sum of the Absolute Value of the Difference between Atomic Polarizabilities of All Bonded Atoms in the Molecule
extractDrugCarbonTypes Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extractDrugChiChain Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extractDrugChiCluster Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6
extractDrugChiPath Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7
extractDrugChiPathCluster Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6
extractDrugCPSA A Variety of Descriptors Combining Surface Area and Partial Charge Information
extractDrugDescOB Calculate Molecular Descriptors Provided by OpenBabel
extractDrugECI Calculate the Eccentric Connectivity Index Descriptor
extractDrugEstate Calculate the E-State Molecular Fingerprints (in Compact Format)
extractDrugEstateComplete Calculate the E-State Molecular Fingerprints (in Complete Format)
extractDrugExtended Calculate the Extended Molecular Fingerprints (in Compact Format)
extractDrugExtendedComplete Calculate the Extended Molecular Fingerprints (in Complete Format)
extractDrugFMF Calculate the FMF Descriptor
extractDrugFragmentComplexity Calculate Complexity of a System
extractDrugGraph Calculate the Graph Molecular Fingerprints (in Compact Format)
extractDrugGraphComplete Calculate the Graph Molecular Fingerprints (in Complete Format)
extractDrugGravitationalIndex Descriptor Characterizing the Mass Distribution of the Molecule.
extractDrugHBondAcceptorCount Number of Hydrogen Bond Acceptors
extractDrugHBondDonorCount Number of Hydrogen Bond Donors
extractDrugHybridization Calculate the Hybridization Molecular Fingerprints (in Compact Format)
extractDrugHybridizationComplete Calculate the Hybridization Molecular Fingerprints (in Complete Format)
extractDrugHybridizationRatio Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States
extractDrugIPMolecularLearning Calculate the Descriptor that Evaluates the Ionization Potential
extractDrugKappaShapeIndices Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices
extractDrugKierHallSmarts Descriptor that Counts the Number of Occurrences of the E-State Fragments
extractDrugKR Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)
extractDrugKRComplete Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)
extractDrugLargestChain Descriptor that Calculates the Number of Atoms in the Largest Chain
extractDrugLargestPiSystem Descriptor that Calculates the Number of Atoms in the Largest Pi Chain
extractDrugLengthOverBreadth Calculate the Ratio of Length to Breadth Descriptor
extractDrugLongestAliphaticChain Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain
extractDrugMACCS Calculate the MACCS Molecular Fingerprints (in Compact Format)
extractDrugMACCSComplete Calculate the MACCS Molecular Fingerprints (in Complete Format)
extractDrugMannholdLogP Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms
extractDrugMDE Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O
extractDrugMomentOfInertia Descriptor that Calculates the Principal Moments of Inertia and Ratios of the Principal Moments
extractDrugOBFP2 Calculate the FP2 Molecular Fingerprints
extractDrugOBFP3 Calculate the FP3 Molecular Fingerprints
extractDrugOBFP4 Calculate the FP4 Molecular Fingerprints
extractDrugOBMACCS Calculate the MACCS Molecular Fingerprints
extractDrugPetitjeanNumber Descriptor that Calculates the Petitjean Number of a Molecule
extractDrugPetitjeanShapeIndex Descriptor that Calculates the Petitjean Shape Indices
extractDrugPubChem Calculate the PubChem Molecular Fingerprints (in Compact Format)
extractDrugPubChemComplete Calculate the PubChem Molecular Fingerprints (in Complete Format)
extractDrugRotatableBondsCount Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule
extractDrugRuleOfFive Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five
extractDrugShortestPath Calculate the Shortest Path Molecular Fingerprints (in Compact Format)
extractDrugShortestPathComplete Calculate the Shortest Path Molecular Fingerprints (in Complete Format)
extractDrugStandard Calculate the Standard Molecular Fingerprints (in Compact Format)
extractDrugStandardComplete Calculate the Standard Molecular Fingerprints (in Complete Format)
extractDrugTPSA Descriptor of Topological Polar Surface Area Based on Fragment Contributions (TPSA)
extractDrugVABC Descriptor that Calculates the Volume of A Molecule
extractDrugVAdjMa Descriptor that Calculates the Vertex Adjacency Information of A Molecule
extractDrugWeight Descriptor that Calculates the Total Weight of Atoms
extractDrugWeightedPath Descriptor that Calculates the Weighted Path (Molecular ID)
extractDrugWHIM Calculate Holistic Descriptors Described by Todeschini et al.
extractDrugWienerNumbers Descriptor that Calculates Wiener Path Number and Wiener Polarity Number
extractDrugXLogP Descriptor that Calculates the Prediction of logP Based on the Atom-Type Method Called XLogP
extractDrugZagrebIndex Descriptor that Calculates the Sum of the Squared Atom Degrees of All Heavy Atoms
extractPCMBLOSUM Generalized BLOSUM and PAM Matrix-Derived Descriptors
extractPCMDescScales Scales-Based Descriptors with 20+ classes of Molecular Descriptors
extractPCMFAScales Generalized Scales-Based Descriptors derived by Factor Analysis
extractPCMMDSScales Generalized Scales-Based Descriptors derived by Multidimensional Scaling
extractPCMPropScales Generalized AA-Properties Based Scales Descriptors
extractPCMScales Generalized Scales-Based Descriptors derived by Principal Components Analysis
extractProtAAC Amino Acid Composition Descriptor
extractProtAPAAC Amphiphilic Pseudo Amino Acid Composition Descriptor
extractProtCTDC CTD Descriptors - Composition
extractProtCTDD CTD Descriptors - Distribution
extractProtCTDT CTD Descriptors - Transition
extractProtCTriad Conjoint Triad Descriptor
extractProtDC Dipeptide Composition Descriptor
extractProtGeary Geary Autocorrelation Descriptor
extractProtMoran Moran Autocorrelation Descriptor
extractProtMoreauBroto Normalized Moreau-Broto Autocorrelation Descriptor
extractProtPAAC Pseudo Amino Acid Composition Descriptor
extractProtPSSM Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence
extractProtPSSMAcc Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance
extractProtPSSMFeature Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)
extractProtQSO Quasi-Sequence-Order (QSO) Descriptor
extractProtSOCN Sequence-Order-Coupling Numbers
extractProtTC Tripeptide Composition Descriptor

-- G --

getCPI Generating Compound-Protein Interaction Descriptors
getDrug Retrieve Drug Molecules in MOL and SMILES Format from Databases
getFASTAFromKEGG Retrieve Protein Sequence in FASTA Format from the KEGG Database
getFASTAFromUniProt Retrieve Protein Sequence in FASTA Format from the UniProt Database
getMolFromCAS Retrieve Drug Molecules in InChI Format from the CAS Database
getMolFromChEMBL Retrieve Drug Molecules in MOL Format from the ChEMBL Database
getMolFromDrugBank Retrieve Drug Molecules in MOL Format from the DrugBank Database
getMolFromKEGG Retrieve Drug Molecules in MOL Format from the KEGG Database
getMolFromPubChem Retrieve Drug Molecules in MOL Format from the PubChem Database
getPDBFromRCSBPDB Retrieve Protein Sequence in PDB Format from RCSB PDB
getPPI Generating Protein-Protein Interaction Descriptors
getProt Retrieve Protein Sequence in various Formats from Databases
getSeqFromKEGG Retrieve Protein Sequence from the KEGG Database
getSeqFromRCSBPDB Retrieve Protein Sequence from RCSB PDB
getSeqFromUniProt Retrieve Protein Sequence from the UniProt Database
getSmiFromChEMBL Retrieve Drug Molecules in SMILES Format from the ChEMBL Database
getSmiFromDrugBank Retrieve Drug Molecules in SMILES Format from the DrugBank Database
getSmiFromKEGG Retrieve Drug Molecules in SMILES Format from the KEGG Database
getSmiFromPubChem Retrieve Drug Molecules in SMILES Format from the PubChem Database

-- O --

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

-- R --

readFASTA Read Protein 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

-- S --

searchDrug Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search
segProt Protein Sequence Segmentation