| aa.at | Residue Found at the Requested Position |
| aa.comp | Amino Acid Composition |
| abundance | Protein Abundance Data |
| acc.dssp | Compute Residue Accessibility and SASA |
| ac.scan | Scan a Protein in Search of Acetylation Sites |
| atom.dpx | Atom Depth Analysis |
| bg.go | Search GO Terms for Background Set |
| ddG.profile | Contribution of a given position to changes in stability |
| ddG.ptm | PDB Model and Change in Stability of a Modified Protein |
| dis.scan | Scan a Protein in Search of Disease-Related PTM Sites |
| dot-get.exepath | Find Full Paths to Executables |
| dot-get.url | Get Web Resource |
| dpx | Atom Depth Analysis |
| env.extract | Sequence Environment Around a Given Position |
| env.matrices | Environment Matrices |
| env.plot | Differential Sequence Environment Plot |
| env.Ztest | Preferred/Avoided Amino Acids Within an Environment |
| find.aaindex | Find the Amino Acid Indexes |
| foldx.assembly | Compute Assembly Free Energy |
| foldx.mut | Compute Changes in Stability (DDG) |
| foldx.stab | Compute Folding Free Energy (DG) |
| get.area | Atomic Solvation Energies. |
| get.go | Get Gene Ontology Annotation |
| get.seq | Import a Protein Sequence from a Database |
| gl.scan | Scan a Protein in Search of OGlcNAc Sites |
| gracefully_fail | Check that Internet Resource Work Properly and Fail... |
| hdfisher.go | Hypothesis-Driven Fisher Test |
| hmeto | Human MetO sites oxidized by hydrogen peroxide treatment. |
| id.features | Features Related to the Protein Entry |
| id.mapping | Identifier Mapping |
| imutant | Compute Changes in Stability (DDG) |
| is.at | Check Residue a Fixed Position |
| kegg.uniprot | Identifier Mapping From KEGG to UniProt |
| me.scan | Scan a Protein in Search of Methylation Sites |
| meto.list | List Proteins Found in MetOSite Matching a Keyword |
| meto.scan | Scans a Protein in Search of MetO Sites |
| meto.search | Search for Specific MetO Sites |
| mkdssp | Compute DSSP File Using an In-House Version of the DSSP... |
| msa | Multiple Sequence Alignment |
| net.go | Gene Ontology Network |
| ni.scan | Scan a Protein in Search of Nitration Sites |
| pairwise.dist | Compute Euclidean Distances |
| parse.dssp | Parse a DSSP File to Return a Dataframe |
| pdb2uniprot | Return the UniProt ID Given the PDB and Chain IDs |
| pdb.chain | Download and/or Split PDB Files. |
| pdb.quaternary | Protein Subunit Composition |
| pdb.select | Select the PDB with the Optimal Coverage to the UniProt... |
| pdb.seq | Get Chain Sequences |
| pdb.uniprot | Identifier Mapping From PDB to UniProt |
| prot2codon | Find the Coding Triplets for a Given Protein |
| p.scan | Scan a Protein in Search of Phosphosites |
| ptm.plot | Plot Values of a Property and PTM Sites Along the Protein... |
| ptm.scan | Scan a Protein in Search of PTM Sites |
| reg.scan | Scan a Protein in Search of Regulatory PTM Sites |
| renum | Renumerate Residue Position |
| renum.meto | Renumerate Residue Position |
| renum.pdb | Renumerate Residue Position |
| res.dpx | Residue Depth Analysis |
| saro.dist | Compute Distances to the Closest Aromatic Residues |
| saro.geometry | Compute Geometric Parameters of S-Aromatic Motifs |
| saro.motif | Search for S-Aromatic Motifs |
| search.go | Search a Simple User Query |
| sni.scan | Scan a Protein in Search of S-nitrosylation Sites |
| species.kegg | Convert Between Species Name and KEGG 3-Letter Code Format |
| species.mapping | Map Protein ID to Species |
| stru.part | Partition of Structural Regions |
| su.scan | Scan a Protein in Search of Sumoylation Sites |
| term.go | Get Core Information About the GO Term |
| ub.scan | Scan a Protein in Search of Ubiquitination Sites |
| uniprot2pdb | Return the PDB and Chain IDs of the Provided UniProt Protein |
| uniprot.kegg | Identifier Mapping From UniProt to KEGG |
| uniprot.pdb | Identifier Mapping From UniProt to PDB |
| xprod | Compute Cross Product |
