DynDom protocols

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 IN pipelines

 (8)
2017
PMCID: 5758874
PMID: 29186528
DOI: 10.1093/nar/gkx1164

[…] 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 (32)., emsa experiments with wt and mutant rcsb proteins were run in 10% acrylamide gel using 0.5× tris/borate/edta (tbe) buffer, containing 4 mm mgcl2, either for gel preparation […]

2016
PMCID: 4760774
PMID: 26895240
DOI: 10.1371/journal.ppat.1005451

[…] in denv3 and residues 274–895 in jev. the rmsds of two structures were calculated using pymol [54]. the conformational differences between the denv and jev ns5 structures were analyzed using the dyndom protein domain motion analysis program [32]. the maximum dimension of the ns5 monomer was calculated by crysol [36]., construction of a full-length cdna of denv2 (new guinea c strain) […]

2013
PMCID: 3693407
PMID: 23778582
DOI: 10.1038/tp.2013.49

[…] were compared by calculating difference binding energies δδg using foldx. dynamic structures were generated using the method of normal and geometric parameters that have been determined with dyndom.19 model structures were visualized using pymol (http://www.pymol.org)., to search for novel genetic variations that may have a functional impact on the kibra protein, we performed a screening […]

2012
PMCID: 3329491
PMID: 22529931
DOI: 10.1371/journal.pone.0034734

[…] program [48] using default parameters. the buried surface areas and contacts between the subunits were calculated with a probe of 1.4 å radius using pisa [49]. subdomain movements were analyzed with dyndom [50]. figures of protein structures were drawn using pymol (http://www.pymol.org)., thermal stability was assessed with the thermofluor approach [17] in 96-well sealed plates using a real-time […]

2011
PMCID: 3102710
PMID: 21637813
DOI: 10.1371/journal.ppat.1002059

[…] surfaces were calculated using program areaimol [60] with a 1.7 å radius sphere as the probe (table 1) and values rounded to the nearest 5 å2. conformational differences were analyzed using the dyndom server (http://www.cmp.uea.ac.uk/dyndom/main.jsp). figures were created using pymol (http://www.pymol.org). the coordinates of the wild-type/sah, mutant, and wild-type/sinefungin structures […]

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

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