| 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 | 
| crossSetSim | Parallel Protein Sequence Similarity Calculation Between Two Sets Based on Sequence Alignment (In-Memory Version) | 
| crossSetSimDisk | Parallel Protein Sequence Similarity Calculation Between Two Sets Based on Sequence Alignment (Disk-Based Version) | 
| extractAAC | Amino Acid Composition Descriptor | 
| extractAPAAC | Amphiphilic Pseudo Amino Acid Composition (APseAAC) Descriptor | 
| extractBLOSUM | BLOSUM and PAM Matrix-Derived Descriptors | 
| extractCTDC | CTD Descriptors - Composition | 
| extractCTDCClass | CTD Descriptors - Composition (with customized amino acid classification support) | 
| extractCTDD | CTD Descriptors - Distribution | 
| extractCTDDClass | CTD Descriptors - Distribution (with customized amino acid classification support) | 
| extractCTDT | CTD Descriptors - Transition | 
| extractCTDTClass | CTD Descriptors - Transition (with customized amino acid classification support) | 
| extractCTriad | Conjoint Triad Descriptor | 
| extractCTriadClass | Conjoint Triad Descriptor (with customized amino acid classification support) | 
| extractDC | Dipeptide Composition Descriptor | 
| extractDescScales | Scales-Based Descriptors with 20+ classes of Molecular Descriptors | 
| extractFAScales | Scales-Based Descriptors derived by Factor Analysis | 
| extractGeary | Geary Autocorrelation Descriptor | 
| extractMDSScales | Scales-Based Descriptors derived by Multidimensional Scaling | 
| extractMoran | Moran Autocorrelation Descriptor | 
| extractMoreauBroto | Normalized Moreau-Broto Autocorrelation Descriptor | 
| extractPAAC | Pseudo Amino Acid Composition (PseAAC) Descriptor | 
| extractProtFP | Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) | 
| extractProtFPGap | Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support | 
| extractPSSM | Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence | 
| extractPSSMAcc | Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance | 
| extractPSSMFeature | Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) | 
| extractQSO | Quasi-Sequence-Order (QSO) Descriptor | 
| extractScales | Scales-Based Descriptors derived by Principal Components Analysis | 
| extractScalesGap | Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support) | 
| extractSOCN | Sequence-Order-Coupling Numbers | 
| extractTC | Tripeptide Composition Descriptor | 
| getUniProt | Retrieve Protein Sequences from UniProt by Protein ID | 
| OptAA3d | OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1) | 
| parGOSim | Protein Similarity Calculation based on Gene Ontology (GO) Similarity | 
| parSeqSim | Parallel Protein Sequence Similarity Calculation Based on Sequence Alignment (In-Memory Version) | 
| parSeqSimDisk | Parallel Protein Sequence Similarity Calculation Based on Sequence Alignment (Disk-Based Version) | 
| protcheck | Protein sequence amino acid type sanity check | 
| protseg | Protein Sequence Segmentation/Partition | 
| readFASTA | Read Protein Sequences in FASTA Format | 
| readPDB | Read Protein Sequences in PDB Format | 
| removeGaps | Remove or replace gaps from protein sequences. | 
| twoGOSim | Protein Similarity Calculation based on Gene Ontology (GO) Similarity | 
| twoSeqSim | Protein Sequence Alignment for Two Protein Sequences |