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DP-Bind specifications

Information


Unique identifier OMICS_03581
Name DP-Bind
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Igor B. Kuznetsov

Publication for DP-Bind

DP-Bind citations

 (22)
library_books

Characterization of the DNA binding activity of structural protein VP1 from chicken anaemia virus

2018
PMCID: 5936033
PMID: 29728113
DOI: 10.1186/s12917-018-1465-5

[…] c region within the N-terminus of VP1 contains high arginine content and might confer an ability to VP1 to bind and protect DNA []. Using online software, including PSORT II (http://psort.hgc.jp) and DP-Bind (lcg.rit.albany.edu/dp-bind/), the VP1 protein was analysed in this study. A total of four putative DNA-binding motifs and two putative NLSs were found and predicted within the CAV VP1, as ill […]

library_books

The mycobacterial phosphatase PtpA regulates the expression of host genes and promotes cell proliferation

2017
Nat Commun
PMCID: 5557760
PMID: 28811474
DOI: 10.1038/s41467-017-00279-z

[…] software suite for ChIP-seq analysis, which was partially created to support this study. MEME motif analysis was used to identify PtpA consensus motifs. DNA-binding residues of PtpA were predicted by DP-bind, a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. The protein–protein interaction network was established by the STRING (Search Tool for the Retrieva […]

library_books

mRNA Quantification of NIPBL Isoforms A and B in Adult and Fetal Human Tissues, and a Potentially Pathological Variant Affecting Only Isoform A in Two Patients with Cornelia de Lange Syndrome

2017
Int J Mol Sci
PMCID: 5372497
PMID: 28241484
DOI: 10.3390/ijms18030481

[…] DP-Bind server (http://lcg.rit.albany.edu/dp-bind), a system for the sequence-based prediction of DNA-binding residues in proteins, suggested that the C-terminal segment of NIPBL isoform A (residues 2 […]

library_books

TIS7 induces transcriptional cascade of methylosome components required for muscle differentiation

2016
BMC Biol
PMCID: 5080701
PMID: 27782840
DOI: 10.1186/s12915-016-0318-6

[…] of this minimal essential region for TIS7-mediated activation of ICln transcription. Using bioinformatics prediction software (DISIS (www.predictprotein.org), BinDN+ (http://bioinfo.ggc.org/bindn+/), DP-Bind (http://lcg.rit.albany.edu/dp-bind/), and DNABindR (http://turing.cs.iastate.edu/PredDNA/); Additional file : Figure S2) we identified, with 70–80 % probability, three distinct DNA-binding dom […]

library_books

Structural basis for LIN54 recognition of CHR elements in cell cycle regulated promoters

2016
Nat Commun
PMCID: 4974476
PMID: 27465258
DOI: 10.1038/ncomms12301

[…] create a structural model for DREAM bound to DNA (). Consistent with reported footprinting data, LIN54 contacts the minor groove and E2F-DP binds the major groove. The model shows that LIN54 and E2F-DP bind the DNA helix on opposite faces. We found that three or four base pairs is the closest the two DNA sequence elements can be without steric clashes between the two bound DBDs.The organization o […]

library_books

Transgelin increases metastatic potential of colorectal cancer cells in vivo and alters expression of genes involved in cell motility

2016
BMC Cancer
PMCID: 4741053
PMID: 26847345
DOI: 10.1186/s12885-016-2105-8

[…] echanism. Transgelin localized partially in the nucleus of the CRC cells; it shares 85 % similarity to TAGLN3, which is believed to be a transcriptional regulator []; Bioinformatic analysis using the DP-bind Web server (http://lcg.rit.albany.edu/dp-bind) identified several segments of transgelin as having high DNA-binding potential (data not shown); studies also suggests that nuclear actin-binding […]

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DP-Bind institution(s)
Gen*NY*Sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY, USA

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