Dataset Information

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

ABSTRACT:

Motivation

Chemical cross-linking with mass spectrometry (XL-MS) provides structural information for proteins and protein complexes in the form of crosslinked residue proximity and distance constraints between reactive residues. Utilizing spatial information derived from cross-linked residues can therefore assist with structural modeling of proteins. Selection of computationally derived model structures of proteins remains a major challenge in structural biology. The comparison of site interactions resulting from XL-MS with protein structure contact maps can assist the selection of structural models.

Availability and implementation

XLmap was implemented in R and is freely available at: http://brucelab.gs.washington.edu/software.php.

Contact

jimbruce@uw.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Schweppe DK

PROVIDER: S-EPMC5013974 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Schweppe Devin K DK Chavez Juan D JD Bruce James E JE

Bioinformatics (Oxford, England) 20150926 2

<h4>Motivation</h4>Chemical cross-linking with mass spectrometry (XL-MS) provides structural information for proteins and protein complexes in the form of crosslinked residue proximity and distance constraints between reactive residues. Utilizing spatial information derived from cross-linked residues can therefore assist with structural modeling of proteins. Selection of computationally derived model structures of proteins remains a major challenge in structural biology. The comparison of site i ...[more]

PMID: 26411867

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Dataset Information

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Motivation

Availability and implementation

Contact

Supplementary information

Publications

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Similar Datasets

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