Analyses of Protein Post-Translational Modifications

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Documentation for package ‘ptm’ version 0.2.6

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.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