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Bioinformatics. 2015 Sep 1;31(17):2801-7. doi: 10.1093/bioinformatics/btv270. Epub 2015 Apr 25.

DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes.

Author information

1
Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

Abstract

MOTIVATION:

Atomic resolution modeling of large multimolecular assemblies is a key task in Structural Cell Biology. Experimental techniques can provide atomic resolution structures of single proteins and small complexes, or low resolution data of large multimolecular complexes.

RESULTS:

We present a novel integrative computational modeling method, which integrates both low and high resolution experimental data. The algorithm accepts as input atomic resolution structures of the individual subunits obtained from X-ray, NMR or homology modeling, and interaction data between the subunits obtained from mass spectrometry. The optimal assembly of the individual subunits is formulated as an Integer Linear Programming task. The method was tested on several representative complexes, both in the bound and unbound cases. It placed correctly most of the subunits of multimolecular complexes of up to 16 subunits and significantly outperformed the CombDock and Haddock multimolecular docking methods.

AVAILABILITY AND IMPLEMENTATION:

http://bioinfo3d.cs.tau.ac.il/DockStar

CONTACT:

naamaamir@mail.tau.ac.il or wolfson@tau.ac.il

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
25913207
DOI:
10.1093/bioinformatics/btv270
[Indexed for MEDLINE]

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