Protein Sequence Retrivial

Functions for retrieving protein sequence data from online databases.

getProt()

Retrieve Protein Sequence in various Formats from Databases

getFASTAFromUniProt()

Retrieve Protein Sequence in FASTA Format from the UniProt Database

getFASTAFromKEGG()

Retrieve Protein Sequence in FASTA Format from the KEGG Database

getPDBFromRCSBPDB()

Retrieve Protein Sequence in PDB Format from RCSB PDB

getSeqFromUniProt()

Retrieve Protein Sequence from the UniProt Database

getSeqFromKEGG()

Retrieve Protein Sequence from the KEGG Database

getSeqFromRCSBPDB()

Retrieve Protein Sequence from RCSB PDB

Drug Molecular Data Retrivial

Functions for retrieving drug molecular data from online databases.

getDrug()

Retrieve Drug Molecules in MOL and SMILES Format from Databases

getMolFromDrugBank()

Retrieve Drug Molecules in MOL Format from the DrugBank Database

getMolFromPubChem()

Retrieve Drug Molecules in MOL Format from the PubChem Database

getMolFromChEMBL()

Retrieve Drug Molecules in MOL Format from the ChEMBL Database

getMolFromKEGG()

Retrieve Drug Molecules in MOL Format from the KEGG Database

getMolFromCAS()

Retrieve Drug Molecules in InChI Format from the CAS Database

getSmiFromDrugBank()

Retrieve Drug Molecules in SMILES Format from the DrugBank Database

getSmiFromPubChem()

Retrieve Drug Molecules in SMILES Format from the PubChem Database

getSmiFromChEMBL()

Retrieve Drug Molecules in SMILES Format from the ChEMBL Database

getSmiFromKEGG()

Retrieve Drug Molecules in SMILES Format from the KEGG Database

Protein Sequence Descriptors

Functions and datasets for computing commonly used protein sequence derived descriptors.

extractProtAAC()

Amino Acid Composition Descriptor

extractProtDC()

Dipeptide Composition Descriptor

extractProtTC()

Tripeptide Composition Descriptor

extractProtMoreauBroto()

Normalized Moreau-Broto Autocorrelation Descriptor

extractProtMoran()

Moran Autocorrelation Descriptor

extractProtGeary()

Geary Autocorrelation Descriptor

extractProtCTDC()

CTD Descriptors - Composition

extractProtCTDT()

CTD Descriptors - Transition

extractProtCTDD()

CTD Descriptors - Distribution

extractProtCTriad()

Conjoint Triad Descriptor

extractProtSOCN()

Sequence-Order-Coupling Numbers

extractProtQSO()

Quasi-Sequence-Order (QSO) Descriptor

extractProtPAAC()

Pseudo Amino Acid Composition Descriptor

extractProtAPAAC()

Amphiphilic Pseudo Amino Acid Composition Descriptor

AAindex

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

Profile-Based Protein Sequence Descriptors

Functions for generating profile-based protein representations.

extractProtPSSM()

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

extractProtPSSMFeature()

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

extractProtPSSMAcc()

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

Scales-Based Descriptors for Proteochemometrics Modeling

Functions for generating scales-based descriptors for proteochemometrics (PCM) modeling.

extractPCMScales()

Generalized Scales-Based Descriptors derived by Principal Components Analysis

extractPCMPropScales()

Generalized AA-Properties Based Scales 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

extractPCMBLOSUM()

Generalized BLOSUM and PAM Matrix-Derived Descriptors

acc()

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

Molecular Descriptor Sets for Generating Scales-Based Descriptors

Molecular descriptor sets of the 20 amino acids for generating scales-based descriptors.

OptAA3d

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

AAMetaInfo

Meta Information for the 20 Amino Acids

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

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

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

AAInfo

Information Indices Descriptors for 20 Amino Acids calculated by Dragon

AAMolProp

Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon

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

AACPSA

CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio

AADescAll

All 2D Descriptors for 20 Amino Acids calculated by Dragon

AAMOE2D

2D Descriptors for 20 Amino Acids calculated by MOE 2011.10

AAMOE3D

3D Descriptors for 20 Amino Acids calculated by MOE 2011.10

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

AABLOSUM100

BLOSUM100 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

AAPAM120

PAM120 Matrix for 20 Amino Acids

AAPAM250

PAM250 Matrix for 20 Amino Acids

Molecular Descriptors

Functions for computing commonly used molecular descriptors.

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

extractDrugFMF()

Calculate the FMF Descriptor

extractDrugFragmentComplexity()

Calculate Complexity of a System

extractDrugGravitationalIndex()

Descriptor Characterizing the Mass Distribution of the Molecule.

extractDrugHBondAcceptorCount()

Number of Hydrogen Bond Acceptors

extractDrugHBondDonorCount()

Number of Hydrogen Bond Donors

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

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

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

extractDrugPetitjeanNumber()

Descriptor that Calculates the Petitjean Number of a Molecule

extractDrugPetitjeanShapeIndex()

Descriptor that Calculates the Petitjean Shape Indices

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

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

Molecular Fingerprints

Functions for computing commonly used molecular fingerprints.

extractDrugStandard()

Calculate the Standard Molecular Fingerprints (in Compact Format)

extractDrugStandardComplete()

Calculate the Standard Molecular Fingerprints (in Complete Format)

extractDrugExtended()

Calculate the Extended Molecular Fingerprints (in Compact Format)

extractDrugExtendedComplete()

Calculate the Extended Molecular Fingerprints (in Complete Format)

extractDrugGraph()

Calculate the Graph Molecular Fingerprints (in Compact Format)

extractDrugGraphComplete()

Calculate the Graph Molecular Fingerprints (in Complete Format)

extractDrugHybridization()

Calculate the Hybridization Molecular Fingerprints (in Compact Format)

extractDrugHybridizationComplete()

Calculate the Hybridization Molecular Fingerprints (in Complete Format)

extractDrugMACCS()

Calculate the MACCS Molecular Fingerprints (in Compact Format)

extractDrugMACCSComplete()

Calculate the MACCS Molecular Fingerprints (in Complete Format)

extractDrugEstate()

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

extractDrugEstateComplete()

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

extractDrugPubChem()

Calculate the PubChem Molecular Fingerprints (in Compact Format)

extractDrugPubChemComplete()

Calculate the PubChem Molecular Fingerprints (in Complete Format)

extractDrugKR()

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

extractDrugKRComplete()

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

extractDrugShortestPath()

Calculate the Shortest Path Molecular Fingerprints (in Compact Format)

extractDrugShortestPathComplete()

Calculate the Shortest Path Molecular Fingerprints (in Complete Format)

extractDrugOBFP2()

Calculate the FP2 Molecular Fingerprints

extractDrugOBFP3()

Calculate the FP3 Molecular Fingerprints

extractDrugOBFP4()

Calculate the FP4 Molecular Fingerprints

extractDrugOBMACCS()

Calculate the MACCS Molecular Fingerprints

PPI and CPI Descriptors

Functions for computing protein-protein and compound-protein interation descriptors.

getPPI()

Generating Protein-Protein Interaction Descriptors

getCPI()

Generating Compound-Protein Interaction Descriptors

Similarity and Similarity Searching

Functions for computing sequence/molecular similarities and similarity searching.

calcDrugFPSim()

Calculate Drug Molecule Similarity Derived by Molecular Fingerprints

calcDrugMCSSim()

Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search

searchDrug()

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

calcTwoProtSeqSim()

Protein Sequence Alignment for Two Protein Sequences

calcParProtSeqSim()

Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment

calcTwoProtGOSim()

Protein Similarity Calculation based on Gene Ontology (GO) Similarity

calcParProtGOSim()

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

Protein Sequence Data Processing

Functions for processing protein sequence data.

readFASTA()

Read Protein Sequences in FASTA Format

readPDB()

Read Protein Sequences in PDB Format

segProt()

Protein Sequence Segmentation

checkProt()

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

Molecular Data Processing

Functions for processing molecular data.

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

convMolFormat()

Chemical File Formats Conversion

Rcpi-package

Toolkit for Compound-Protein Interaction in Drug Discovery