.get.exepath            Find Full Paths to Executables
.get.url                Get Web Resource
aa.at                   Residue Found at the Requested Position
aa.comp                 Amino Acid Composition
abundance               Protein Abundance Data
ac.scan                 Scan a Protein in Search of Acetylation Sites
acc.dssp                Compute Residue Accessibility and SASA
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
dpx                     Atom Depth Analysis
env.Ztest               Preferred/Avoided Amino Acids Within an
                        Environment
env.extract             Sequence Environment Around a Given Position
env.matrices            Environment Matrices
env.plot                Differential Sequence Environment Plot
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 Gracefully When Not
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 Software
msa                     Multiple Sequence Alignment
net.go                  Gene Ontology Network
ni.scan                 Scan a Protein in Search of Nitration Sites
p.scan                  Scan a Protein in Search of Phosphosites
pairwise.dist           Compute Euclidean Distances
parse.dssp              Parse a DSSP File to Return a Dataframe
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 Sequence
pdb.seq                 Get Chain Sequences
pdb.uniprot             Identifier Mapping From PDB to UniProt
pdb2uniprot             Return the UniProt ID Given the PDB and Chain
                        IDs
prot2codon              Find the Coding Triplets for a Given Protein
ptm.plot                Plot Values of a Property and PTM Sites Along
                        the Protein Sequence
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
uniprot.kegg            Identifier Mapping From UniProt to KEGG
uniprot.pdb             Identifier Mapping From UniProt to PDB
uniprot2pdb             Return the PDB and Chain IDs of the Provided
                        UniProt Protein
xprod                   Compute Cross Product
