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Rcpi (version 1.8.0)

Toolkit for Compound-Protein Interaction in Drug Discovery

Description

The Rcpi package offers an R/Bioconductor package emphasizing the comprehensive integration of bioinformatics and chemoinformatics into a molecular informatics platform for drug discovery.

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Version

Version

1.8.0

License

Artistic-2.0

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/road2stat/Rcpi

Maintainer

Nan Xiao

Last Published

February 15th, 2017

Functions in Rcpi (1.8.0)

PAM70 Matrix for 20 Amino Acids

Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon

BLOSUM50 Matrix for 20 Amino Acids

BLOSUM100 Matrix for 20 Amino Acids

BLOSUM62 Matrix for 20 Amino Acids

extractDrugChiPathCluster

Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6

extractDrugEstate

Calculate the E-State Molecular Fingerprints (in Compact Format)

calcParProtGOSim

Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity

2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon

Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon

GETAWAY Descriptors for 20 Amino Acids calculated by Dragon

PAM30 Matrix for 20 Amino Acids

AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids

RDF Descriptors for 20 Amino Acids calculated by Dragon

calcParProtSeqSim

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment

PAM120 Matrix for 20 Amino Acids

extractDrugGraph

Calculate the Graph Molecular Fingerprints (in Compact Format)

Geometrical Descriptors for 20 Amino Acids calculated by Dragon

extractDrugIPMolecularLearning

Calculates the Descriptor that Evaluates the Ionization Potential

Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon

Check if the protein sequence's amino acid types are the 20 default types

Calculates the FMF Descriptor

All 2D Descriptors for 20 Amino Acids calculated by Dragon

extractDrugChiCluster

Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6

BLOSUM45 Matrix for 20 Amino Acids

extractDrugApol

Calculates the Sum of the Atomic Polarizabilities Descriptor

extractDrugAminoAcidCount

Calculates the Number of Amino Acids Descriptor

extractDrugAutocorrelationMass

Calculates the Moreau-Broto Autocorrelation Descriptors using Atomic Weight

Calculate Drug Molecule Similarity Derived by Molecular Fingerprints

extractDrugHybridizationComplete

Calculate the Hybridization Molecular Fingerprints (in Complete Format)

extractDrugKRComplete

Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)

Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O

extractDrugBCUT

BCUT -- Eigenvalue Based Descriptor

extractDrugHybridization

Calculate the Hybridization Molecular Fingerprints (in Compact Format)

extractDrugBondCount

Calculates the Descriptor Based on the Number of Bonds of a Certain Bond Order

extractDrugPetitjeanShapeIndex

Descriptor that Calculates the Petitjean Shape Indices

extractDrugPubChem

Calculate the PubChem Molecular Fingerprints (in Compact Format)

extractDrugDescOB

Calculate Molecular Descriptors Provided by OpenBabel

extractDrugLengthOverBreadth

Calculates the Ratio of Length to Breadth Descriptor

extractDrugStandardComplete

Calculate the Standard Molecular Fingerprints (in Complete Format)

extractDrugLargestChain

Descriptor that Calculates the Number of Atoms in the Largest Chain

Calculates the Eccentric Connectivity Index Descriptor

extractDrugHBondAcceptorCount

Descriptor that Calculates the Number of Hydrogen Bond Acceptors

extractDrugAutocorrelationCharge

Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges

extractDrugOBFP2

Calculate the FP2 Molecular Fingerprints

extractDrugShortestPathComplete

Calculate the Shortest Path Molecular Fingerprints (in Complete Format)

extractDrugShortestPath

Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

extractProtPSSM

Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence

extractDrugZagrebIndex

Descriptor that Calculates the Sum of the Squared Atom Degrees of All Heavy Atoms

extractDrugExtended

Calculate the Extended Molecular Fingerprints (in Compact Format)

extractDrugMACCSComplete

Calculate the MACCS Molecular Fingerprints (in Complete Format)

extractDrugTPSA

Descriptor of Topological Polar Surface Area Based on Fragment Contributions (TPSA)

extractDrugRotatableBondsCount

Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule

extractDrugWHIM

Calculate Holistic Descriptors Described by Todeschini et al.

3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon

extractDrugGraphComplete

Calculate the Graph Molecular Fingerprints (in Complete Format)

extractProtCTriad

Conjoint Triad Descriptor

getSeqFromRCSBPDB

Retrieve Protein Sequence from RCSB PDB

extractProtCTDT

CTD Descriptors - Transition

extractPCMScales

Generalized Scales-Based Descriptors derived by Principal Components Analysis

getMolFromPubChem

Retrieve Drug Molecules in MOL Format from the PubChem Database

extractDrugXLogP

Descriptor that Calculates the Prediction of logP Based on the Atom-Type Method Called XLogP

extractProtCTDD

CTD Descriptors - Distribution

Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search

extractPCMBLOSUM

Generalized BLOSUM and PAM Matrix-Derived Descriptors

BLOSUM80 Matrix for 20 Amino Acids

Tripeptide Composition Descriptor

extractDrugMACCS

Calculate the MACCS Molecular Fingerprints (in Compact Format)

Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)

Generating Protein-Protein Interaction Descriptors

Topological Descriptors for 20 Amino Acids calculated by Dragon

extractDrugPetitjeanNumber

Descriptor that Calculates the Petitjean Number of a Molecule

extractProtSOCN

Sequence-Order-Coupling Numbers

extractDrugRuleOfFive

Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five

Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon

extractDrugBPol

Calculates the Descriptor that Describes the Sum of the Absolute Value of the Difference between Atomic Polarizabilities of All Bonded Atoms in the Molecule

extractPCMMDSScales

Generalized Scales-Based Descriptors derived by Multidimensional Scaling

getSeqFromUniProt

Retrieve Protein Sequence from the UniProt Database

extractProtPAAC

Pseudo Amino Acid Composition Descriptor

getPDBFromRCSBPDB

Retrieve Protein Sequence in PDB Format from RCSB PDB

getMolFromDrugBank

Retrieve Drug Molecules in MOL Format from the DrugBank Database

Retrieve Drug Molecules in SMILES Format from the KEGG Database

extractDrugChiChain

Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7

extractDrugVAdjMa

Descriptor that Calculates the Vertex Adjacency Information of A Molecule

extractProtAPAAC

Amphiphilic Pseudo Amino Acid Composition Descriptor

Retrieve Protein Sequence from the KEGG Database

Read Molecules from SDF Files and Return Parsed Java Molecular Object

getMolFromChEMBL

Retrieve Drug Molecules in MOL Format from the ChEMBL Database

extractProtMoran

Moran Autocorrelation Descriptor

extractProtPSSMFeature

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

Dipeptide Composition Descriptor

Quasi-Sequence-Order (QSO) Descriptor

Retrieve Drug Molecules in InChI Format from the CAS Database

getSmiFromChEMBL

Retrieve Drug Molecules in SMILES Format from the ChEMBL Database

getSmiFromDrugBank

Retrieve Drug Molecules in SMILES Format from the DrugBank Database

getSmiFromPubChem

Retrieve Drug Molecules in SMILES Format from the PubChem Database

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

PAM250 Matrix for 20 Amino Acids

Toolkit for Compound-Protein Interaction in Drug Discovery

extractDrugChiPath

Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7

extractDrugGravitationalIndex

Descriptor Characterizing the Mass Distribution of the Molecule.

extractPCMPropScales

Generalized AA-Properties Based Scales Descriptors

extractDrugWienerNumbers

Descriptor that Calculates Wiener Path Number and Wiener Polarity Number

Protein Sequence Segmentation

Retrieve Drug Molecules in MOL Format from the KEGG Database

extractProtGeary

Geary Autocorrelation Descriptor

Constitutional Descriptors for 20 Amino Acids calculated by Dragon

3D Descriptors for 20 Amino Acids calculated by MOE 2011.10

Meta Information for the 20 Amino Acids

Information Indices Descriptors for 20 Amino Acids calculated by Dragon

Calculates All the Molecular Descriptors in the Rcpi Package at Once

extractDrugLongestAliphaticChain

Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain

extractPCMFAScales

Generalized Scales-Based Descriptors derived by Factor Analysis

extractPCMDescScales

Scales-Based Descriptors with 20+ classes of Molecular Descriptors

extractDrugPubChemComplete

Calculate the PubChem Molecular Fingerprints (in Complete Format)

Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List

Read Protein Sequences in FASTA Format

Read Protein Sequences in PDB Format

Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon

2D Descriptors for 20 Amino Acids calculated by MOE 2011.10

Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon

Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon

WHIM Descriptors for 20 Amino Acids calculated by Dragon

calcTwoProtSeqSim

Protein Sequence Alignment for Two Protein Sequences

extractDrugALOGP

Calculates Atom Additive logP and Molar Refractivity Values Descriptor

extractDrugExtendedComplete

Calculate the Extended Molecular Fingerprints (in Complete Format)

extractDrugCPSA

A Variety of Descriptors Combining Surface Area and Partial Charge Information

extractDrugLargestPiSystem

Descriptor that Calculates the Number of Atoms in the Largest Pi Chain

extractDrugOBMACCS

Calculate the MACCS Molecular Fingerprints

extractDrugKierHallSmarts

Descriptor that Counts the Number of Occurrences of the E-State Fragments

extractDrugMomentOfInertia

Descriptor that Calculates the Principal Moments of Inertia and Ratios of the Principal Moments

extractDrugKappaShapeIndices

Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices

extractProtCTDC

CTD Descriptors - Composition

Generating Compound-Protein Interaction Descriptors

Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon

CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio

extractDrugAromaticAtomsCount

Calculates the Number of Aromatic Atoms Descriptor

extractDrugAtomCount

Calculates the Number of Atom Descriptor

extractDrugAromaticBondsCount

Calculates the Number of Aromatic Bonds Descriptor

extractDrugMannholdLogP

Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms

extractDrugHBondDonorCount

Descriptor that Calculates the Number of Hydrogen Bond Donors

extractDrugOBFP4

Calculate the FP4 Molecular Fingerprints

extractDrugStandard

Calculate the Standard Molecular Fingerprints (in Compact Format)

extractDrugWeight

Descriptor that Calculates the Total Weight of Atoms

Amino Acid Composition Descriptor

extractDrugHybridizationRatio

Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States

extractProtMoreauBroto

Normalized Moreau-Broto Autocorrelation Descriptor

getFASTAFromUniProt

Retrieve Protein Sequence in FASTA Format from the UniProt Database

Retrieve Protein Sequence in various Formats from Databases

Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon

Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon

calcTwoProtGOSim

Protein Similarity Calculation based on Gene Ontology (GO) Similarity

PAM40 Matrix for 20 Amino Acids

Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length

Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search

Chemical File Formats Conversion

extractDrugCarbonTypes

Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization

extractDrugEstateComplete

Calculate the E-State Molecular Fingerprints (in Complete Format)

extractDrugFragmentComplexity

Calculate Complexity of a System

extractDrugAutocorrelationPolarizability

Calculates the Moreau-Broto Autocorrelation Descriptors using Polarizability

extractDrugOBFP3

Calculate the FP3 Molecular Fingerprints

extractDrugVABC

Descriptor that Calculates the Volume of A Molecule

extractDrugWeightedPath

Descriptor that Calculates the Weighted Path (Molecular ID)

extractProtPSSMAcc

Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance

Retrieve Drug Molecules in MOL and SMILES Format from Databases

getFASTAFromKEGG

Retrieve Protein Sequence in FASTA Format from the KEGG Database