tCONCOORD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool tCONCOORD
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Tool usage distribution map

This map represents all the scientific publications referring to tCONCOORD per scientific context
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Associated diseases

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Protocols

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

Versioning


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This tool is not available anymore.

Publications for tCONCOORD

tCONCOORD citations

 (15)
library_books

Predicting Protein Dynamics and Allostery Using Multi Protein Atomic Distance Constraints

2017
PMCID: 5343748
PMID: 28190781
DOI: 10.1016/j.str.2017.01.008

[…] tCONCOORD () is run with default parameters. NMSim is run via the NMSim web server () with the default parameters for large-scale motions. This produces five trajectories of 500 structures. Every tent […]

call_split

Binding of Myomesin to Obscurin Like 1 at the Muscle M Band Provides a Strategy for Isoform Specific Mechanical Protection

2017
PMCID: 5222588
PMID: 27989621
DOI: 10.1016/j.str.2016.11.015
call_split See protocol

[…] ATSAS package (). Initial rigid body modeling of the complex was done with CORAL () and domain dynamics of the protein complexes was further explored by generating conformational ensembles using the tCONCOORD () method. Further details are available in the . […]

library_books

The Gearbox of the Bacterial Flagellar Motor Switch

2016
PMCID: 4938800
PMID: 27345932
DOI: 10.1016/j.str.2016.05.012

[…] rom the PDB. Secondary structure elements and the contact interface within the FliMMFliGMC complex (PDB: 4FHR) are mapped in . Component structures (monomers and partial complexes) are described in . tCONCOORD produced a conformational ensemble from each X-ray structure. First, atomic pair distances with upper and lower limits were generated from the structure based on tables of bonding interactio […]

library_books

Ligand Docking to Intermediate and Close To Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

2016
PLoS One
PMCID: 4922591
PMID: 27348230
DOI: 10.1371/journal.pone.0158063

[…] 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 to the k […]

library_books

Substrate Specificity, Inhibitor Selectivity and Structure Function Relationships of Aldo Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase

2015
PLoS One
PMCID: 4519324
PMID: 26222439
DOI: 10.1371/journal.pone.0134506

[…] e protein, parameters of Holmberg et al. [] for the cofactor, and Generalized-Born implicit solvent model with parameters of Hawkins et al. []. The minimized structures were used as the input for the tCONCOORD algorithm [], which generates a set of independent conformations based on geometrical constraints []. It was designed to accurately capture the protein flexibility and the validity of the re […]

library_books

Highly specific ubiquitin competing molecules effectively promote frataxin accumulation and partially rescue the aconitase defect in Friedreich ataxia cells

2015
PMCID: 4358773
PMID: 25549872
DOI: 10.1016/j.nbd.2014.12.011

[…] s 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 (). […]


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

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