DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes

G C P van Zundert; A M J J Bonvin

doi:10.1093/bioinformatics/btv333

DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes

Bioinformatics. 2015 Oct 1;31(19):3222-4. doi: 10.1093/bioinformatics/btv333. Epub 2015 May 29.

Authors

G C P van Zundert¹, A M J J Bonvin¹

Affiliation

¹ Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, The Netherlands.

Abstract

We present DisVis, a Python package and command line tool to calculate the reduced accessible interaction space of distance-restrained binary protein complexes, allowing for direct visualization and quantification of the information content of the distance restraints. The approach is general and can also be used as a knowledge-based distance energy term in FFT-based docking directly during the sampling stage.

Availability and implementation: The source code with documentation is freely available from https://github.com/haddocking/disvis.

Contact: a.m.j.j.bonvin@uu.nl

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computer Graphics*
Data Interpretation, Statistical*
Proteasome Endopeptidase Complex / metabolism*
Protein Interaction Maps
Protein Subunits
RNA Polymerase II / chemistry
RNA Polymerase II / metabolism*
Saccharomyces cerevisiae / metabolism
Software*

Substances

Protein Subunits
RNA Polymerase II
Proteasome Endopeptidase Complex
ATP dependent 26S protease