Recognition of small molecule-RNA binding sites using RNA sequence and structure.

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