RNABPDB: Molecular Modeling of RNA Structure—From Base Pair Analysis in Crystals to Structure Prediction

• Published in: Interdisciplinary sciences : computational life sciences 2022-09, Vol.14 (3), p.759-774
• Main Authors: Mukherjee, Debasish, Maiti, Satyabrata, Gouda, Prasanta Kumar, Sharma, Richa, Roy, Parthajit, Bhattacharyya, Dhananjay
• Format: Article
• Language: English
• Subjects: Base pairs; Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computational Science and Engineering; Computer Appl. in Life Sciences; Crystal structure; Crystals; Dimensional stability; Estimation; Gene regulation; Health Sciences; Helices; Life Sciences; Mathematical and Computational Physics; Mathematical models; Medicine; miRNA; Modelling; Molecular modelling; Molecular structure; Original Research Article; Parameters; Post-transcription; Ribonucleic acid; RNA; Servers; Statistics for Life Sciences; Theoretical; Theoretical and Computational Chemistry
• ISSN: 1913-2751; 1867-1462
• DOI: 10.1007/s12539-022-00528-w

The stable three-dimensional structure of RNA is known to play several important biochemical roles, from post-transcriptional gene regulation to enzymatic action. These structures contain double-helical regions, which often have different types of non-canonical base pairs in addition to Watson–Crick base pairs. Hence, it is important to study their structures from experimentally obtained or even predicted ones, to understand their role, or to develop a drug against the potential targets. Molecular Modeling of RNA double helices containing non-canonical base pairs is a difficult process, particularly due to the unavailability of structural features of non-Watson–Crick base pairs. Here we show a composite web-server with an associated database that allows one to generate the structure of RNA double helix containing non-canonical base pairs using consensus parameters obtained from the database. The database classification is followed by an evaluation of the central tendency of the structural parameters as well as a quantitative estimation of interaction strengths. These parameters are used to construct three-dimensional structures of double helices composed of Watson–Crick and/or non-canonical base pairs. Our benchmark study to regenerate double-helical fragments of many experimentally derived RNA structures indicate very high accuracy. This composite server is expected to be highly useful in understanding functions of various pre-miRNA by modeling structures of the molecules and estimating binding efficiency. The database can be accessed from http://hdrnas.saha.ac.in/rnabpdb . Graphical Abstract