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tCONCOORD specifications

Information


Unique identifier OMICS_09804
Name tCONCOORD
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publications for tCONCOORD

tCONCOORD in publications

 (10)
PMCID: 5343748
PMID: 28190781
DOI: 10.1016/j.str.2017.01.008

[…] apo/holo pairs it is shown that existing coarse-grained methods often cannot span large conformational changes. for t4-lysozyme, exprose is able to generate ensembles that are more native-like than tconcoord and nmsim, and comparable with targeted md. by adding additional constraints representing potential modulators, exprose can predict allosteric sites. exprose ranks an allosteric pocket […]

PMCID: 5222588
PMID: 27989621
DOI: 10.1016/j.str.2016.11.015

[…] than that seen in the crystal. we then used this structure as a starting template and, following energy minimization, generated >30,000 additional models (a selection shown in c) using the tconcoord () algorithm, a computationally efficient method for sampling conformational transitions. within this large pool, we found ∼500 models that provide an excellent fit (χ < 1.0) […]

PMCID: 4938800
PMID: 27345932
DOI: 10.1016/j.str.2016.05.012

[…] (). alternatively, it could be due to intrinsic flexibility, with the two rotation states generated by conformational selection as found for binding of adp to the f0f1 atp synthase (). we used tconcoord to discriminate between these alternatives. tconcoord generates atomic-detail conformational ensembles from a single structure based on distance constraints (). detection of labile hydrogen […]

PMCID: 4922591
PMID: 27348230
DOI: 10.1371/journal.pone.0158063

[…] satisfactory results in ligand docking., we will particularly mention two studies on the prediction of holo structures in hinge-bending proteins. first one is a biased sampling procedure with tconcoord [] that was applied on 10 monomeric proteins exhibiting closure of two domains. by imposing the holo structure’s rg on the tconcoord ensemble, global backbone rmsd of the best model […]

PMCID: 4358773
PMID: 25549872
DOI: 10.1016/j.nbd.2014.12.011

[…] v. 4.6.5 to add missing atoms and to refine the models. side chains flexibility was investigated with the program reduce. the refined crystal structure was used to generate 1000 protein models with tconcoord ()., the experimentally determined models of frataxin were used to investigate the location of putative binding pockets on the solvent accessible surface of the protein using metapocket (), […]


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tCONCOORD institution(s)
Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

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