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DP-dock specifications


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 citations


Evidence supporting a critical contribution of intrinsically disordered regions to the biochemical behavior of full length human HP1γ

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

[…] predictions are in agreement with experimental data [], though no details of these interactions currently exist at the atomic resolution level. Subsequently, we sought confirmation of this finding by DP-Dock, another independent unbiased prediction approach, which uses different rules and 3D structural models as input. An added value of DP-Dock is that, if successful, it would allow the generation […]


Evidence supporting the existence of a NUPR1 like family of helix loop helix chromatin proteins related to, yet distinct from, AT hook containing HMG proteins

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

[…] homology-based approach is shown in Fig. . This complex was maintained through ionic, van der Waals, and hydrogen-bonding interactions, which are represented graphically in Fig. . The second method, DP-Dock, uses a nonspecific B-DNA to probe the binding site on a 3D model of a protein that is known to bind DNA but for which the specific amino acid to nucleic acid base contacts are unknown. Given […]


Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans

Nucleic Acids Res
PMCID: 3902906
PMID: 24121681
DOI: 10.1093/nar/gkt902

[…] A combination of machine learning (DP-bind) and rigid docking (DP-dock) algorithms were used to derive ab initio inferences regarding the DNA binding residues of CsoRSl (,). The Venn diagram in A illustrates a strong consensus prediction between the two programs, […]

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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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