Recognition of small molecule-RNA binding sites using RNA sequence and structure.
Ontology highlight
ABSTRACT: Motivation
RNA molecules become attractive small-molecule drug targets to treat disease in recent years. Computer-aided drug design can be facilitated by detecting the RNA sites that bind small molecules. However, very limited progress has been reported for the prediction of small molecule-RNA binding sites.Results
We developed a novel method RNAsite to predict small molecule-RNA binding sites using sequence profile- and structure-based descriptors. RNAsite was shown to be competitive with the state-of-the-art methods on the experimental structures of two independent test sets. When predicted structure models were used, RNAsite outperforms other methods by a large margin. The possibility of improving RNAsite by geometry-based binding pocket detection was investigated. The influence of RNA structure's flexibility and the conformational changes caused by ligand binding on RNAsite were also discussed. RNAsite is anticipated to be a useful tool for the design of RNA-targeting small molecule drugs.Availability and implementation
http://yanglab.nankai.edu.cn/RNAsite.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Su H
PROVIDER: S-EPMC8034527 | biostudies-literature |
REPOSITORIES: biostudies-literature
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