RBRDetector – Prediction of Binding Residues on RNA-binding Protein Structures

RBRDetector

:: DESCRIPTION

RBRDetector is a novel structure-based algorithm to identify RNA-binding residues by combining feature- and template-based prediction strategies.

::DEVELOPER

Rong Liu’s Lab of Protein Bioinformatics at Huazhong Agriculture University!

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2014 Oct;82(10):2455-71. doi: 10.1002/prot.24610. Epub 2014 Jun 9.
RBRDetector: Improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies.
Yang XX1, Deng ZL, Liu R.

RNABindRPlus 1.0 – Prediction of RNA-binding Residues in Protein

RNABindRPlus 1.0

:: DESCRIPTION

RNABindRPlus predicts RNA-binding residues from protein sequences by combining the output from a Support Vector Machine (SVM) classifier with the output from a Homology-based method.

::DEVELOPER

Artificial Intelligence Research Laboratory and Dobbs Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.
Walia RR, Xue LC, Wilkins K, El-Manzalawy Y, Dobbs D, Honavar V.
PLoS One. 2014 May 20;9(5):e97725. doi: 10.1371/journal.pone.0097725

BindN / BindN+ / BindN-RF – Sequence-based Prediction of DNA and RNA-binding

BindN / BindN+ / BindN-RF

:: DESCRIPTION

BindN applies support vector machines (SVMs) to prediction of DNA and RNA-binding residues from sequence features, including the side chain pKa value, hydrophobicity index and molecular mass of an amino acid.

BindN+, an upgraded version of BindN, applies support vector machines (SVMs) to sequence-based prediction of DNA or RNA-binding residues from biochemical features and evolutionary information.

BindN-RF applies Random Forests (RFs) to sequence-based prediction of DNA-binding residues in proteins using biochemical features and evolutionary information.

::DEVELOPER

Clemson University Department of Genetics and Biochemistry and Greenwood Genetic Center.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang, L. and Brown, S.J. (2006)
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences.
Nucleic Acids Res., 34:W243-W248.

BMC Syst Biol. 2010 May 28;4 Suppl 1:S3. doi: 10.1186/1752-0509-4-S1-S3.
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features.
Wang L1, Huang C, Yang MQ, Yang JY.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S1. doi: 10.1186/1471-2164-10-S1-S1.
Prediction of DNA-binding residues from protein sequence information using random forests.
Wang L1, Yang MQ, Yang JY.