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CombDock specifications

Information


Unique identifier OMICS_23984
Name CombDock
Alternative name COMBinatorial assembly by multiple DOCKing
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yuval Inbar

Publication for COMBinatorial assembly by multiple DOCKing

CombDock citations

 (5)
library_books

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

2016
PLoS Comput Biol
PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] . Adaptations of these methods to extend their applicability to the multimeric setting are neither trivial nor obvious.Early work by Nussinov and colleagues introduced a greedy, systematic algorithm, CombDock, for the problem of multimeric docking [,]. The algorithm is general and can handle heteromeric and asymmetric complexes but is challenged by the combinatorial explosion in the number of dime […]

library_books

Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces

2015
Proteins
PMCID: 5049452
PMID: 26248608
DOI: 10.1002/prot.24873

[…] urden. DockTrina also exploits the idea to reward implicitly produced interfaces compatible with pregenerated docking poses, and does not rely on advance information on interaction interfaces. Unlike CombDock, which does not require information on these interfaces either, we explicitly use such information to assemble a complex by successive attachment of monomers and perform a greedy search in or […]

library_books

HopDock: a probabilistic search algorithm for decoy sampling in protein protein docking

2013
Proteome Sci
PMCID: 3909090
PMID: 24564839
DOI: 10.1186/1477-5956-11-S1-S6

[…] ts of the moving unit onto the base unit.Nowadays, many protein-protein docking software and web servers are available, such as pyDock [], Haddock [], Zdock [], ClusPro [], PatchDock and SymmDock [], Combdock [], Budda [], Rosetta-Dock [], SKE-DOCK [], FiberDock [], and more. As summaries of their performance in the Critical Assessment of PRedicted Interactions (CAPRI) community-wide experiment ar […]

call_split

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

2011
Int J Mol Sci
PMCID: 3083708
PMID: 21541061
DOI: 10.3390/ijms12021316
call_split See protocol

[…] complexes with composite interface, starting from the results of an initial set of two-body docking simulations [,,]. The algorithm was initially developed to performing multi-macromolecular docking (CombDock [,], which requires the resolution of a highly complex combinatorial search problem. The only difference with flexible hinge domain docking is that specific restraints were added to the proce […]

library_books

Structural assembly of two domain proteins by rigid body docking

2008
BMC Bioinformatics
PMCID: 2579442
PMID: 18925951
DOI: 10.1186/1471-2105-9-441

[…] en some solutions with ligand RMSD above 10 Å that are still acceptable (e.g. 2 cases in target T32, and 1 case in target T36).Inbar et al. [] recently described their combinatorial docking approach (CombDock) for multi-domain and multi-molecular assembly. However, they reported only three cases of domain-domain docking (the other reported cases were either docking of secondary structure elements […]

Citations

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CombDock institution(s)
School of Computer Science, Tel Aviv University, Tel Aviv, Israel; Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Basic Research Program, SAIC-Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI - FCRDC, Frederick, MD, USA
CombDock funding source(s)
Supported by the ‘Center of Excellence in Geometric Computing and its Applications’ funded by the Israel Science Foundation (administered by the Israel Academy of Sciences) and by grants of Tel Aviv University Basic Research Foundation, by the Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University, by the Eshkol Fellowship funded by the Israeli Ministry of Science and by Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400.

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