Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
- 1Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- 2Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- 3European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- 4Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- 5Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire CNRS, Architecture et Réactivité de l'ARN, 67084 Strasbourg, France
- Corresponding author: mszachniuk{at}cs.put.poznan.pl
Abstract
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1052 RNA 3D structures, including 1030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analyzed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity, or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modeling approaches.
Keywords
- Received January 16, 2021.
- Accepted November 5, 2021.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
