DynDom protocols

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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 in pipelines

 (10)
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 ()., 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 []. the conformational differences between the denv and jev ns5 structures were analyzed using the dyndom protein domain motion analysis program []. the maximum dimension of the ns5 monomer was calculated by crysol []., construction of a full-length cdna of denv2 (new guinea c strain) and its ns5 […]

2016
PMCID: 5001606
PMID: 27307602
DOI: 10.1093/nar/gkw543

[…] the assignment of atomic charge and radius information with pdb2pqr (). all structural representations were prepared with pymol (schrödinger, llc). protein domain motions were analyzed using dyndom (). the coordinates and structure factors have been deposited in the protein data bank with id 5d8c (wild-type hinmlr:padhc-estd/nmlr(wt) dna complex); 5e01 (wild-type […]

2015
PMCID: 4569070
PMID: 26366880
DOI: 10.1371/journal.pcbi.1004346

[…] simulations., to identify the collective motions of the whole fg molecule and of its subdomains we performed several principal component analyses (pca) [] using wordom [] and gromacs utilities []. dyndom [] was used to identify rigid domains and hinges of motion. the overlap between spaces spanned by the dominant pca modes of different simulations was used to quantify the similarity […]

2014
PMCID: 3985705
PMID: 24433110
DOI: 10.1021/bi401525h

[…] the ha2 domains were aligned at ha2 residues 37–55 and ha2 residues 76–110. the orientation of the r domain was calculated by the dyndomain server (http://fizz.cmp.uea.ac.uk/dyndom/)., the solvent accessible surface area (sasa) was analyzed by using interprosurf server (http://curie.utmb.edu/prosurf.html). the ha1–ha1 interface area was calculated by the formula […]


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DynDom in publications

 (107)
PMCID: 5945598
PMID: 29749375
DOI: 10.1038/s41467-018-04290-w

[…] the final rigid body of the id. the rigid body of sd1 (7–35, 68–137, 337–372) was also determined by the same method., 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. ., we constructed models of cofilins bound to the f-sites, go-sites, and gi-sites (fig. ) on f-actin (fig. ). […]

PMCID: 5931139
PMID: 29717994
DOI: 10.1107/S2053230X18004557

[…] 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., […]

PMCID: 5750235
PMID: 29295972
DOI: 10.1038/s41467-017-02312-7

[…] 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 […]

PMCID: 5741831
PMID: 29175998
DOI: 10.1042/BSR20171399

[…] 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 []., hsp104 and variants (0.5 µm monomer) were incubated with 2 mm atp at 22°c for 15 min. the amount of released inorganic phosphate was measured using the malachite green assay []., firefly […]

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 ()., 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 […]


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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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