Rcpi Quick Reference Card

Nan Xiao <https://nanx.me>

2018-04-30

1 Retrieve Protein Sequence Data from Online Databases

Table 1: Retrieving protein sequence data from various online databases
Function name Function description
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

2 Retrieve Drug Molecular Data from Online Databases

Table 2: Retrieving drug molecular data from various online databases
Function name Function description
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

3 Calculate Commonly Used Protein Sequence Derived Descriptors

Table 3: Calculating commonly used protein sequence derived descriptors
Function name Descriptor name Descriptor group
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

4 Generate Profile-Based Protein Representations

Table 4: Generating profile-based protein representations
Function name Function description
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)

5 Generate Scales-Based Descriptors for Proteochemometrics Modeling

Table 5: Generating scales-based descriptors for proteochemometrics modeling
Function name Descriptor class Derived by
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

6 Molecular Descriptor Sets of the 20 Amino Acids for Generating Scales-Based Descriptors

Table 6: Pre-calculated molecular descriptor sets of the 20 amino acids in for generating scales-based descriptors for proteochemometrics modeling.
Dataset name Dataset description Dimensionality Calculated by
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

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

7 Molecular Descriptors

Table 7: Molecular descriptors
Function name Descriptor name
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

8 Molecular Fingerprints

Table 8: Molecular fingerprints
Function name Fingerprint type
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

9 Protein-Protein and Compound-Protein Interation Descriptors

Table 9: Protein-protein and compound-protein interation descriptors
Function name Function description
getPPI() Generating protein-protein interaction descriptors
getCPI() Generating compound-protein interaction descriptors

10 Similarity and Similarity Searching

Table 10: Similarity and similarity searching
Function name Function description
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

11 Protein Sequence Data Manipulation

Table 11: Protein sequence data manipulation
Function name Function description
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

12 Molecular Data Manipulation

Table 12: Molecular data manipulation
Function name Function description
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