RNABindR

[…] Potential RNA-binding sites were searched in the HEX 110 sequence using RNABindR, BindN, PPRint, SVM and RNABindRPlus softwares [–]. We selected the most significant motifs, and only the alignments passing a threshold of 80% were considered as significant. The cNLS Mapper […]

[…] Li lab and Xiaoyong Pan provided RNAProSite and xypan prediction results respectively, with default parameter. aaRNA was used by inputting the structure file with default parameters. RNABindR and RNABindRPlus were predicted with default parameters, while removing 95% sequence identity in RNABindRPlus. KYG was predicted with command line using “method_type = 8” option. RBscore_SVM […]

[…] plex structures (since June 2012). The prediction results of each method in these two datasets were presented in the . The accuracy of all the methods in both datasets lies between 55–71%. BindN+ and RNABindR v2.0 showed the best performance in both datasets at the distance cutoff of ≤3.5 Å and ≤6.0 Å, respectively. Pprint and NAPS performed well with an average accuracy of 66% and 61%, respective […]

[…] dues in protein sequences. For example, BindN [] uses a support vector machine (SVM) to predict the RNA- or DNA-binding residues in a protein sequence based on the chemical properties of amino acids. RNABindR [,] predicts the RNA-binding residues in a protein sequence using a Naïve Bayes classifier. However, none of these consider interacting partners (i.e., RNA) for a given protein when predictin […]

[…] alignment. Terribilini et al. (2006) [] applied a Naïve Bayes classifier with amino acid sequence information for predicting RNA interacting residues and presented the results through the web service RNABindR []. The ability to computationally predict RNA-binding residues in a RNA-binding protein can help biologists reveal site-directed mutagenesis in wet-lab experiments.Caragea et al. [] explored […]

[…] 3D (http://sunserver.cdfd.org.in:8080/protease/PAR_3D/access.html) was used, though none was identified . 6) Putative RNA binding residues were identified using BindN (http://bioinfo.ggc.org/bindn/), RNAbindR (http://bindr.gdcb.iastate.edu/RNABindR/), and KYG (http://yayoi.kansai.jaea.go.jp/qbg/kyg/index.php) –. 7) Conserved residues were mapped onto the structure using ConSurf . 8) For phylogenet […]