DNABind

[…] 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 […]

[…] 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. […]

[…] 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. […]

[…] % 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, […]

[…] 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 […]

[…] 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 […]