MetBP: a software tool for detection of interaction between metal ion–RNA base pairs

Abstract

Abstract Motivation The role of metals in shaping and functioning of RNA is a well-established fact, and the understanding of that through the analysis of structural data has biological relevance. Often metal ions bind to one or more atoms of the nucleobase of an RNA. This fact becomes more interesting when such bases form a base pair with any other base. Furthermore, when metal ions bind to any residue of an RNA, the secondary structural features of the residue (helix, loop, unpaired, etc.) are also biologically important. The available metal-binding-related software tools cannot address such type-specific queries. Results To fill this limitation, we have designed a software tool, called MetBP that meets the goal. This tool is a stand-alone command-line-based tool and has no dependency on the other existing software. It accepts a structure file in mmCIF or PDB format and computes the base pairs and thereafter reports all metals that bind to one or more nucleotides that form pairs with another. It reports binding distance, angles along with base pair stability. It also reports several other important aspects, e.g. secondary structure of the residue in the RNA. MetBP can be used as a generalized metal-binding site detection tool for Proteins and DNA as well. Availability and implementation https://github.com/computational-biology/metbp Supplementary information Supplementary data are available at Bioinformatics online.