.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 |