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

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...

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Vydáno v:Bioinformatics Ročník 31; číslo 17; s. 2801 - 2807
Hlavní autoři: Amir, Naama, Cohen, Dan, Wolfson, Haim J.
Médium: Journal Article
Jazyk:angličtina
Vydáno: England 01.09.2015
Témata:
Algorithms
Animals
Assemblies
Atomic properties
Atomic structure
Bioinformatics
Cattle
Computational Biology - methods
Humans
Mathematical models
Models, Molecular
Molecular Docking Simulation
Multiprotein Complexes - chemistry
Protein Conformation
Proteins
Proteins - chemistry
Saccharomyces cerevisiae Proteins
Structural Homology, Protein
Tasks
ISSN:1367-4803, 1367-4811, 1460-2059
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Shrnutí: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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ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv270