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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)Systematic classification of the His Me finger superfamily
[…] 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 […]
De novo protein function prediction using DNA binding and RNA binding proteins as a test case
[…] 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. […]
Potential DNA binding and nuclease functions of ComEC domains characterized in silico
[…] 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. […]
A Large Scale Assessment of Nucleic Acids Binding Site Prediction Programs
[…] % 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, […]
A property based analysis of human transcription factors
[…] 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 […]
A Conserved C Terminal Domain of the Aspergillus fumigatus Developmental Regulator MedA Is Required for Nuclear Localization, Adhesion and Virulence
[…] 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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