# Analyses of Protein Post-Translational Modifications

## Documentation for package ‘ptm’ version 0.2.6

- DESCRIPTION file.
- Package NEWS.

## Help Pages

.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.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 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