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DynDom specifications

Information


Unique identifier OMICS_05556
Name DynDom
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for DynDom

DynDom citations

 (132)
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Structural basis for cofilin binding and actin filament disassembly

2018
Nat Commun
PMCID: 5945598
PMID: 29749375
DOI: 10.1038/s41467-018-04290-w
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[…] The rotation axes of domain movement were obtained by the DomainSelect program (DynDom) based on the two rigid bodies shown in Supplementary Table  and Fig. . […]

library_books

A cryoprotectant induces conformational change in glyceraldehyde 3 phosphate dehydrogenase

2018
PMCID: 5931139
PMID: 29717994
DOI: 10.1107/S2053230X18004557

[…] and R cryst factors of 20.5% and 18.4%, respectively (Table 3). Structure validation was performed with SFCHECK (Vaguine et al., 1999), PROCHECK (Laskowski et al., 1996) and ADIT (Bhat et al., 2001). DynDom, a program that determines domain movement and relative inter-domain rotation angles in proteins for which two conformations are available, was used to study domain rotation (Poornam et al., 20 […]

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Trapping IgE in a closed conformation by mimicking CD23 binding prevents and disrupts FcεRI interaction

2018
Nat Commun
PMCID: 5750235
PMID: 29295972
DOI: 10.1038/s41467-017-02312-7
call_split See protocol

[…] 3 domain with a distance restraint of 25 Å. Calculation of the angle of rotation between the SAXS models and the extended (RCSB: 4J4P) and bent (RCSB: 2WQR) conformation of IgE Fc was performed using DynDom. Ensemble optimization of both unbound IgE Fc and the IgE Fc:026 sdab complex was performed using the EOM 2.0 programs RANCH and GAJOE. A total of 5000 models were generated utilizing the same […]

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Structural determinants for protein unfolding and translocation by the Hsp104 protein disaggregase

2017
Biosci Rep
PMCID: 5741831
PMID: 29175998
DOI: 10.1042/BSR20171399
call_split See protocol

[…] rried out using COOT [] and PHENIX [], respectively. Atomic coordinates and structure factors have been deposited in the PDB with the accession number 5WBW. Protein domain motions were analyzed using DynDom []. […]

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Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator

2017
Nucleic Acids Res
PMCID: 5758874
PMID: 29186528
DOI: 10.1093/nar/gkx1164
call_split See protocol

[…] or S207C–RcsBAC structure showed 95.5% of residues in favored and 4.5% in allowed region. The figures were produced using PyMOL (http://www.pymol.org) and the movement analysis was performed with the Dyndom program (). […]

library_books

The molecular basis of phosphite and hypophosphite recognition by ABC transporters

2017
Nat Commun
PMCID: 5700983
PMID: 29170493
DOI: 10.1038/s41467-017-01226-8

[…] d binding data were similar to the other phosphite-binding proteins discussed previously. Analysis of the conformational change between the open and closed, phosphite-bound structure of Ps_PtxB using DynDom revealed that domain closure is induced by a ~60° rotation around an axis that lies between the two lobes (Fig. ). This is facilitated by flexible loops that form the hinge region between the l […]

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DynDom institution(s)
D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, UK

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