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 in publications

 (5)
PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] 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 […]

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

[…] up to 24 monomers. methods not relying on symmetry information also exist: docktrina can compute asymmetric trimers by scanning combinations of protein dimers via an rmsd‐based test; mdock_hex and combdock use pairwise dockings to compute clash‐free minimum‐weight spanning trees (based on docking scores) representing protein complexes. other methods employ genetic algorithms and monte‐carlo […]

PMCID: 3083708
PMID: 21541061
DOI: 10.3390/ijms12021316

[…] 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 […]

PMCID: 2938057
PMID: 20305088
DOI: 10.1074/mcp.M000051-MCP201

[…] symmetries. m-zdock and symmdock are suited for the prediction of macromolecules with cyclic symmetries. however, the ability to deal with arbitrary large molecular assemblies is currently rare. combdock (), which was developed by the team of symmdock, can build hetero-oligomer complexes, but it does not have a symmetry option. only haddock can deal with molecular complexes […]

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

[…] 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 […]


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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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