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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| Published in: | Bioinformatics Vol. 31; no. 17; pp. 2801 - 2807 |
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| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
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England
01.09.2015
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| ISSN: | 1367-4803, 1367-4811, 1460-2059 |
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| 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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| AbstractList | 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. MOTIVATIONAtomic 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.RESULTSWe 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 IMPLEMENTATIONhttp://bioinfo3d.cs.tau.ac.il/DockStarCONTACTnaamaamir@mail.tau.ac.il or wolfson@tau.ac.ilSUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. 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 Supplementary information: Supplementary data are available at Bioinformatics online. 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. 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. http://bioinfo3d.cs.tau.ac.il/DockStar naamaamir@mail.tau.ac.il or wolfson@tau.ac.il Supplementary data are available at Bioinformatics online. |
| Author | Amir, Naama Cohen, Dan Wolfson, Haim J. |
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| CitedBy_id | crossref_primary_10_1016_j_str_2015_10_013 crossref_primary_10_1002_jcc_26016 crossref_primary_10_1371_journal_pcbi_1005937 crossref_primary_10_1109_TVCG_2019_2934333 crossref_primary_10_1016_j_bpj_2015_11_3519 crossref_primary_10_1107_S1600576717008172 crossref_primary_10_1038_s41598_017_09654_8 |
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| Snippet | Motivation: Atomic resolution modeling of large multimolecular assemblies is a key task in Structural Cell Biology. Experimental techniques can provide atomic... Atomic resolution modeling of large multimolecular assemblies is a key task in Structural Cell Biology. Experimental techniques can provide atomic resolution... MOTIVATIONAtomic resolution modeling of large multimolecular assemblies is a key task in Structural Cell Biology. Experimental techniques can provide atomic... |
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| SubjectTerms | 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 |
| Title | DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes |
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