Amir N, Cohen D, Wolfson HJ. DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes.
Bioinformatics 2015;
31:2801-7. [PMID:
25913207 DOI:
10.1093/bioinformatics/btv270]
[Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/19/2015] [Indexed: 12/24/2022] Open
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.
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