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Contact networks in RNA: a structural bioinformatics study with a new tool

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Abstract

Base pairing in RNA are significantly rich and versatile due to the potential non-canonical base pairing amongst nucleotides. Not only that, one base in RNA can pair with more than one bases simultaneously. This opens up a new dimension of research to detect such types of base-base pair networks in RNA and to analyze them. Even if a base do not form a pair, it may have significant extent of \(\pi\)-\(\pi\) stacking overlap that can stabilize the structures. In this work, we report a software tool, called BPNet, that accepts a mmCIF or PDB file and computes the base-pair/\(\pi\)-\(\pi\) contact network components using graph formalism. The software can run on Linux platform in both serial and parallel modes. It generates several information in suitable file formats for visualization of the networks. This paper describes the BPNet software and also presents some interesting results obtained by analyzing several RNA structures by the software to show its effectiveness.

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Data Availability

BPNet is Available at: https://github.com/computational-biology/bpnet;branch:master

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Acknowledgements

Authors are thankful to Dr. Debasish Mukherjee, Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany for his contribution to I/O subsystem of BPFIND.

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Authors and Affiliations

  1. Department of Computer Science, The University of Burdwan, Burdwan, West Bengal, 713104, India

    Parthajit Roy

  2. Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India

    Dhananjay Bhattacharyya

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  1. Parthajit Roy
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  2. Dhananjay Bhattacharyya
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Correspondence to Dhananjay Bhattacharyya.

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Roy, P., Bhattacharyya, D. Contact networks in RNA: a structural bioinformatics study with a new tool. J Comput Aided Mol Des 36, 131–140 (2022). https://doi.org/10.1007/s10822-021-00438-x

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