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

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...

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Bibliographic Details
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
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Summary: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
ISSN:1913-2751
1867-1462
DOI:10.1007/s12539-022-00528-w