DP-dock specifications

Information


Unique identifier OMICS_03573
Name DP-dock
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for DP-dock

DP-dock in publications

 (4)
PMCID: 5055493
PMID: 27650952
DOI: 10.1007/s13238-016-0317-y

[…] and a larger one on pilz domain (fig. f). crystal packing analysis helps us to identify the mrkh dimer in which makes two separated regions merge into a long region suitable for dna binding. we used dp-dock (tuszynska et al., ) to predict a mrkh/dna model and the result shows that the interactions between predicted dna-binding regions and double-stranded dna are appropriate (fig. h). we propose […]

PMCID: 4683166
PMID: 26680990
DOI: 10.1007/s00894-015-2874-z

[…] were calculated in the receptor-ligand function of discovery studio client 4.1 using the default parameters []. the three-dimensional complex structure of hp1γ bound to b-dna was generated by using dp-dock [], which has been well validated by our laboratory and others []. dp-dock uses a nonspecific b-dna model to probe the binding site on a 3d model of a protein that is known to bind dna, […]

PMCID: 4139591
PMID: 25056123
DOI: 10.1007/s00894-014-2357-7

[…] complex structure of nupr1a bound with b-dna was generated by docking the nupr1a model into the minor groove of dna to achieve maximal intermolecular interactions between the two partners using dp-dock []. intermolecular interactions of the nupr1–dna complex, including salt bridge interactions, hydrogen bonds, electrostatic interactions, and hydrophobic interactions, were calculated […]

PMCID: 3902906
PMID: 24121681
DOI: 10.1093/nar/gkt902

[…] that csorsl binding drives a ‘conformational switching’ in the operator dna that is dependent on the inherent deformability brought about by the g/c-tracts within the operator site., dp-bind () and dp-dock () were used to predict putative dna binding residues from the amino acid sequence and crystal structure, respectively, of csorsl (). dp-bind derives a consensus prediction from three […]


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DP-dock institution(s)
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA, USA

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