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Protocols

RBscore specifications

Information


Unique identifier OMICS_08394
Name RBscore
Alternative name RNA Binding score
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 1.0
Stability No
Maintained No

Maintainer


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Publication for RNA Binding score

RBscore citations

 (3)
library_books

RBscoreandNBench: a high level web server for nucleic acid binding residues prediction with a large scale benchmarking database

2016
Nucleic Acids Res
PMCID: 4987871
PMID: 27084939
DOI: 10.1093/nar/gkw251

[…] Several normalization steps were processed before calculating RBscore: (i) alternative locations are cleaned leaving only the first state; (ii) residues with incomplete backbone atoms (N, CA and C) are dropped; (iii) Selenomethionines are taken as methionine, wh […]

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

[…] 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 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 S […]

library_books

Phylogenomics and sequence structure function relationships in the GmrSD family of Type IV restriction enzymes

2015
BMC Bioinformatics
PMCID: 4619093
PMID: 26493560
DOI: 10.1186/s12859-015-0773-z

[…] server []. The best scoring models reported by the server were chosen. For GmrS domain restraints on the protein interface were applied, based on the prediction of DNA binding residues done using the RBscore server [] and based on the analysis of sequence conservation. The docked DNA structure is the idealized B-DNA model provided in the NPdock server example data.The distribution of electrostatic […]

Citations

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RBscore institution(s)
Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Strasbourg, France
RBscore funding source(s)
French Government [ANR-10-BINF-02–02 <BACNET>]

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