mkdssp

Computes the DSSP file using an in-house version of the DSSP software.

Contains utilities for the analysis of post-translational modifications (PTMs) in proteins,
with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download,
filter and analyze data from the sulfoxidation database 'MetOSite', and integrate data from other main PTMs
(other databases). Utilities to search and characterize S-aromatic motifs in proteins are also provided.
In addition, functions to analyze sequence environments around modifiable residues in proteins can be found.
For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable
residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
these differential sequence environments are also implemented. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).

Juan Aledo

Analyses of Protein Post-Translational Modifications

Juan Carlos Aledo

mkdssp function

<dl><dt>pdb</dt>
<dd>is either a 4-character identifier of the PDB structure, or the path to a pdb file.</dd>
<dt>method</dt>
<dd>a character string specifying the desired method to get the dssp dataframe; it should be one of 'ptm' or 'bio3d'.</dd>
<dt>exefile</dt>
<dd>file path to the DSSP executable on your system (i.e. how is DSSP invoked).</dd></dl>

Arguments

Author

Compute DSSP File Using an In-House Version of the DSSP Software — mkdssp

<dl>

<dt>pdb</dt>
<dd>is either a 4-character identifier of the PDB structure, or the path to a pdb file.</dd>


<dt>method</dt>
<dd>a character string specifying the desired method to get the dssp dataframe; it should be one of 'ptm' or 'bio3d'.</dd>


<dt>exefile</dt>
<dd>file path to the DSSP executable on your system (i.e. how is DSSP invoked).</dd>

</dl>

mkdssp: Compute DSSP File Using an In-House Version of the DSSP Software

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples