XLMap-package: Map protein cross-links sites to protein structure contact...

In mammmals/XLmap: Map Protein Cross-Link Sites To Protein Structure Contact Maps

Description

Package designed to overlay a protein structure contact map and residues cross-linked within a protein for visualization of cross-linked residues and to calculate the agreement between these two maps. to quantify the degree of overlap.

Details

Package:	XLMap
Type:	Package
Version:	0.1.4
Date:	2015-08-12
License:	GPL-2

Required inputs are: (1) a text file containing cross-linked protein identifications and the sites of cross-linking and, (2) a '.pdb' file containing structural information for the queried protein. The text file should have at least four columns: 'prot1' 'prot2' 'mod_pos1' 'mod_pos2' These specify the protein to be used (e.g. by Uniprot Accession, 'P23284') and the positions within that protein that are interacting. As long as the columns are specified as described, contact map generation and scores can parse the input protein accession from tables containing interactions within and amongst multiple proteins.

Author(s)

Devin K Schweppe, PhD
Maintainer: Devin K Schweppe <[e-mail]>

References

Schweppe et al.

mammmals/XLmap documentation built on May 21, 2019, 11:22 a.m.