In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Retrieve protein sequence data from online databases

Function name Function description

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getProt() Retrieve protein sequence in FASTA format or PDB format from various online databases getFASTAFromUniProt() Retrieve protein sequence in FASTA format from UniProt getFASTAFromKEGG() Retrieve protein sequence in FASTA format from KEGG getPDBFromRCSBPDB() Retrieve protein sequence in PDB Format from RCSB PDB getSeqFromUniProt() Retrieve protein sequence from UniProt getSeqFromKEGG() Retrieve protein sequence from KEGG getSeqFromRCSBPDB() Retrieve protein sequence from RCSB PDB

: Table 1: Retrieving protein sequence data from various online databases

Retrieve drug molecular data from online databases

Function name Function description

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getDrug() Retrieve drug molecules in MOL format and SMILES format from various online databases getMolFromDrugBank() Retrieve drug molecules in MOL format from DrugBank getMolFromPubChem() Retrieve drug molecules in MOL format from PubChem getMolFromChEMBL() Retrieve drug molecules in MOL format from ChEMBL getMolFromKEGG() Retrieve drug molecules in MOL format from the KEGG getMolFromCAS() Retrieve drug molecules in InChI format from CAS getSmiFromDrugBank() Retrieve drug molecules in SMILES format from DrugBank getSmiFromPubChem() Retrieve drug molecules in SMILES format from PubChem getSmiFromChEMBL() Retrieve drug molecules in SMILES format from ChEMBL getSmiFromKEGG() Retrieve drug molecules in SMILES format from KEGG

: Table 2: Retrieving drug molecular data from various online databases

Calculate commonly used protein sequence derived descriptors

Function name Descriptor name Descriptor group

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extractProtAAC() Amino acid composition Amino acid composition extractProtDC() Dipeptide composition extractProtTC() Tripeptide composition extractProtMoreauBroto() Normalized Moreau-Broto autocorrelation Autocorrelation extractProtMoran() Moran autocorrelation extractProtGeary() Geary autocorrelation extractProtCTDC() Composition CTD extractProtCTDT() Transition extractProtCTDD() Distribution extractProtCTriad() Conjoint Triad Conjoint Triad extractProtSOCN() Sequence-order-coupling number Quasi-sequence-order extractProtQSO() Quasi-sequence-order descriptors extractProtPAAC() Pseudo-amino acid composition Pseudo-amino acid composition extractProtAPAAC() Amphiphilic pseudo-amino acid composition AAindex AAindex data of 544 physicochemical and biological properties for 20 amino acids Dataset

: Table 3: Calculating commonly used protein sequence derived descriptors

Generate profile-based protein representations

Function name Function description

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extractProtPSSM() Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence or peptides extractProtPSSMFeature() Profile-based protein representation derived by PSSM extractProtPSSMAcc() Profile-based protein representation derived by PSSM and auto cross covariance (ACC)

: Table 4: Generating profile-based protein representations

Generate scales-based descriptors for proteochemometrics modeling

Function name Descriptor class Derived by

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extractPCMScales() Generalized scales-based descriptors derived by principal components analysis (PCA) Principal components analysis extractPCMPropScales() Generalized scales-based descriptors derived by amino acid properties (AAindex)
extractPCMDescScales() Generalized scales-based descriptors derived by 2D and 3D molecular descriptors (Topological, WHIM, VHSE, etc.)
extractPCMFAScales() Generalized scales-based descriptors derived by factor analysis Factor analysis extractPCMMDSScales() Generalized scales-based descriptors derived by multidimensional scaling (MDS) Multidimensional scaling extractPCMBLOSUM() Generalized BLOSUM and PAM matrix-derived descriptors Substitution matrix acc() Auto cross covariance (ACC) for generating scales-based descriptors of the same length

: Table 5: Generating scales-based descriptors for proteochemometrics modeling

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

Dataset name Dataset description Dimensionality Calculated by

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OptAA3d Optimized 20 amino acids – MOE AA2DACOR 2D autocorrelations descriptors 92 Dragon AA3DMoRSE 3D-MoRSE descriptors 160 Dragon AAACF Atom-centred fragments descriptors 6 Dragon AABurden Burden Eigenvalues descriptors 62 Dragon AAConn Connectivity indices descriptors 33 Dragon AAConst Constitutional descriptors 23 Dragon AAEdgeAdj Edge adjacency indices descriptors 97 Dragon AAEigIdx Eigenvalue-based indices descriptors 44 Dragon AAFGC Functional group counts descriptors 5 Dragon AAGeom Geometrical descriptors 41 Dragon AAGETAWAY GETAWAY descriptors 194 Dragon AAInfo Information indices descriptors 47 Dragon AAMolProp Molecular properties descriptors 12 Dragon AARandic Randic molecular profiles descriptors 41 Dragon AARDF RDF descriptors 82 Dragon AATopo Topological descriptors 78 Dragon AATopoChg Topological charge indices descriptors 15 Dragon AAWalk Walk and path counts descriptors 40 Dragon AAWHIM WHIM descriptors 99 Dragon AACPSA CPSA descriptors 41 Accelrys Discovery Studio AADescAll All the 2D descriptors calculated by Dragon 1171 Dragon AAMOE2D All the 2D descriptors calculated by MOE 148 MOE AAMOE3D All the 3D descriptors calculated by MOE 143 MOE AABLOSUM45 BLOSUM45 matrix for 20 amino acids $20 \times 20$ Biostrings AABLOSUM50 BLOSUM50 matrix for 20 amino acids $20 \times 20$ Biostrings AABLOSUM62 BLOSUM62 matrix for 20 amino acids $20 \times 20$ Biostrings AABLOSUM80 BLOSUM80 matrix for 20 amino acids $20 \times 20$ Biostrings AABLOSUM100 BLOSUM100 matrix for 20 amino acids $20 \times 20$ Biostrings AAPAM30 PAM30 matrix for 20 amino acids $20 \times 20$ Biostrings AAPAM40 PAM40 matrix for 20 amino acids $20 \times 20$ Biostrings AAPAM70 PAM70 matrix for 20 amino acids $20 \times 20$ Biostrings AAPAM120 PAM120 matrix for 20 amino acids $20 \times 20$ Biostrings AAPAM250 PAM250 matrix for 20 amino acids $20 \times 20$ Biostrings

: Table 6: Pre-calculated molecular descriptor sets of the 20 amino acids in for generating scales-based descriptors for proteochemometrics modeling.

Note: non-informative descriptors (e.g. descriptors with only one value across all the 20 amino acids) in these datasets have been filtered out.

Molecular descriptors

Function name Descriptor name

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extractDrugAIO() All the molecular descriptors in the package extractDrugALOGP() Atom additive logP and molar refractivity values descriptor extractDrugAminoAcidCount() Number of amino acids extractDrugApol() Sum of the atomic polarizabilities extractDrugAromaticAtomsCount() Number of aromatic atoms extractDrugAromaticBondsCount() Number of aromatic bonds extractDrugAtomCount() Number of atom descriptor extractDrugAutocorrelationCharge() Moreau-Broto autocorrelation descriptors using partial charges extractDrugAutocorrelationMass() Moreau-Broto autocorrelation descriptors using atomic weight extractDrugAutocorrelationPolarizability() Moreau-Broto autocorrelation descriptors using polarizability extractDrugBCUT() BCUT, the eigenvalue based descriptor extractDrugBondCount() Number of bonds of a certain bond order extractDrugBPol() 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() Kier & Hall Chi chain indices of orders 3, 4, 5, 6 and 7 extractDrugChiCluster() Kier & Hall Chi cluster indices of orders 3, 4, 5 and 6 extractDrugChiPath() Kier & Hall Chi path indices of orders 0 to 7 extractDrugChiPathCluster() Kier & Hall Chi path cluster indices of orders 4, 5 and 6 extractDrugCPSA() Descriptors combining surface area and partial charge information extractDrugDescOB() Molecular descriptors provided by OpenBabel extractDrugECI() Eccentric connectivity index descriptor extractDrugFMF() FMF descriptor extractDrugFragmentComplexity() Complexity of a system extractDrugGravitationalIndex() Mass distribution of the molecule extractDrugHBondAcceptorCount() Number of hydrogen bond acceptors extractDrugHBondDonorCount() Number of hydrogen bond donors extractDrugHybridizationRatio() Molecular complexity in terms of carbon hybridization states extractDrugIPMolecularLearning() Ionization potential extractDrugKappaShapeIndices() Kier & Hall Kappa molecular shape indices extractDrugKierHallSmarts() Number of occurrences of the E-State fragments extractDrugLargestChain() Number of atoms in the largest chain extractDrugLargestPiSystem() Number of atoms in the largest Pi chain extractDrugLengthOverBreadth() Ratio of length to breadth descriptor extractDrugLongestAliphaticChain() Number of atoms in the longest aliphatic chain extractDrugMannholdLogP() LogP based on the number of carbons and hetero atoms extractDrugMDE() Molecular Distance Edge (MDE) descriptors for C, N and O extractDrugMomentOfInertia() Principal moments of inertia and ratios of the principal moments extractDrugPetitjeanNumber() Petitjean number of a molecule extractDrugPetitjeanShapeIndex() Petitjean shape indices extractDrugRotatableBondsCount() Number of non-rotatable bonds on a molecule extractDrugRuleOfFive() Number failures of the Lipinski’s Rule Of Five extractDrugTPSA() Topological Polar Surface Area (TPSA) extractDrugVABC() Volume of a molecule extractDrugVAdjMa() Vertex adjacency information of a molecule extractDrugWeight() Total weight of atoms extractDrugWeightedPath() Weighted path (Molecular ID) extractDrugWHIM() Holistic descriptors described by Todeschini et al. extractDrugWienerNumbers() Wiener path number and wiener polarity number extractDrugXLogP() Prediction of logP based on the atom-type method called XLogP extractDrugZagrebIndex() Sum of the squared atom degrees of all heavy atoms

: Table 7: Molecular descriptors

Molecular fingerprints

Function name Fingerprint type

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extractDrugStandard() Standard molecular fingerprints (in compact format) extractDrugStandardComplete() Standard molecular fingerprints (in complete format) extractDrugExtended() Extended molecular fingerprints (in compact format) extractDrugExtendedComplete() Extended molecular fingerprints (in complete format) extractDrugGraph() Graph molecular fingerprints (in compact format) extractDrugGraphComplete() Graph molecular fingerprints (in complete format) extractDrugHybridization() Hybridization molecular fingerprints (in compact format) extractDrugHybridizationComplete() Hybridization molecular fingerprints (in complete format) extractDrugMACCS() MACCS molecular fingerprints (in compact format) extractDrugMACCSComplete() MACCS molecular fingerprints (in complete format) extractDrugEstate() E-State molecular fingerprints (in compact format) extractDrugEstateComplete() E-State molecular fingerprints (in complete format) extractDrugPubChem() PubChem molecular fingerprints (in compact format) extractDrugPubChemComplete() PubChem molecular fingerprints (in complete format) extractDrugKR() KR (Klekota and Roth) molecular fingerprints (in compact format) extractDrugKRComplete() KR (Klekota and Roth) molecular fingerprints (in complete format) extractDrugShortestPath() Shortest Path molecular fingerprints (in compact format) extractDrugShortestPathComplete() Shortest Path molecular fingerprints (in complete format) extractDrugOBFP2() FP2 molecular fingerprints extractDrugOBFP3() FP3 molecular fingerprints extractDrugOBFP4() FP4 molecular fingerprints extractDrugOBMACCS() MACCS molecular fingerprints

: Table 8: Molecular fingerprints

Protein-protein and compound-protein interation descriptors

Function name Function description

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getPPI() Generating protein-protein interaction descriptors getCPI() Generating compound-protein interaction descriptors

: Table 9: Protein-protein and compound-protein interation descriptors

Similarity and similarity searching

Function name Function description

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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() Similarity calculation based on sequence alignment for a pair of protein sequences calcParProtSeqSim() Parallellized protein sequence similarity calculation based on sequence alignment calcTwoProtGOSim() Similarity calculation based on Gene Ontology (GO) similarity between two proteins calcParProtGOSim() Protein similarity calculation based on Gene Ontology (GO) similarity

: Table 10: Similarity and similarity searching

Protein sequence data manipulation

Function name Function description

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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

: Table 11: Protein sequence data manipulation

Molecular data manipulation

Function name Function description

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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

: Table 12: Molecular data manipulation

nanxstats/Rcpi documentation built on July 6, 2023, 9:57 a.m.