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DNABind specifications

Information


Unique identifier OMICS_07139
Name DNABind
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for DNABind

DNABind citations

 (7)
library_books

Systematic classification of the His Me finger superfamily

2017
Nucleic Acids Res
PMCID: 5714182
PMID: 29040665
DOI: 10.1093/nar/gkx924

[…] to the AlbA superfamily of DNA/RNA-binding domains (). The molecular function of DUF4357 and DUF4268 remains unknown. According to our sequence-based predictions of their DNA-binding potential using DNABIND server (), only DUF4268 is likely (with 98% probability) to bind DNA. Apart from REases, group 3 contains bacterial putative extracellular nucleases containing transmembrane helices and a C-te […]

library_books

De novo protein function prediction using DNA binding and RNA binding proteins as a test case

2016
Nat Commun
PMCID: 5121330
PMID: 27869118
DOI: 10.1038/ncomms13424

[…] t of Dr PIP.To allow for a more detailed comparison of precision-recall curves, we focused on methods that give numerical scores rather than binary classification. We submitted our own set of DBPs to DNABIND and DNAbinder. The PRC is shown in . Dr PIP performance on the non-redundant dataset significantly exceeds the other methods. […]

library_books

Potential DNA binding and nuclease functions of ComEC domains characterized in silico

2016
Proteins
PMCID: 5031224
PMID: 27318187
DOI: 10.1002/prot.25088

[…] iterations of PSI‐BLAST with an E‐value of 0.0001. The models, along with comparator crystal structures of known function were submitted to the structure‐based nucleic acid binding prediction servers DNABIND, and iDBPs. […]

call_split

A Large Scale Assessment of Nucleic Acids Binding Site Prediction Programs

2015
PLoS Comput Biol
PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639
call_split See protocol

[…] % sequence identity in RNABindRPlus. KYG was predicted with command line using “method_type = 8” option. RBscore_SVM was based on the training set of R246. DBS-PSSM, DBS-Pred, RBRIdent, PPRInt, PRBR, DNABind, RBRDetector and ProteDNA were used with default parameter. The DISPLAR program was provided by Sanbo Qin and was run with default parameters. BindN and BindN+ were used by default parameters, […]

library_books

A property based analysis of human transcription factors

2015
BMC Res Notes
PMCID: 4373352
PMID: 25890365
DOI: 10.1186/s13104-015-1039-6

[…] ied, whereas rare cases are more likely to be missed.Some predictions were checked in more detail, based on high FP/FN rates or large differences in Sn and PPV. This involved three domain types (LAG1-DNAbind (PF09271), BTD (PF09272), and HNF-1_N (PF04814)), and two of these (PF09271 and PF09272) did illustrate a potential problem, as there was one predicted continuous DBD overlapping two Pfam doma […]

library_books

A Conserved C Terminal Domain of the Aspergillus fumigatus Developmental Regulator MedA Is Required for Nuclear Localization, Adhesion and Virulence

2012
PLoS One
PMCID: 3503810
PMID: 23185496
DOI: 10.1371/journal.pone.0049959

[…] localization signal, but also the necessary sequences to govern gene expression either through directly binding DNA or interacting with other proteins. A bioinformatics analysis of MedA346–557 using DNABIND and NCBI BLAST revealed no DNA-binding domain in MedA, although it is possible that MedA346–557 contains novel amino acid sequences for the recognition of DNA. A more plausible hypothesis how […]

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DNABind institution(s)
Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA

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