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Article


Title

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

Authors

[ 1 ] Instytut Informatyki, Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ P ] employee

Scientific discipline (Law 2.0)

[2.3] Information and communication technology

Year of publication

2022

Published in

RNA

Journal year: 2022 | Journal volume: vol. 28 | Journal number: no. 2

Article type

scientific article

Publication language

english

Keywords
EN
  • stereochemistry
  • quality validation
  • RNA structure
  • 3D structure prediction
  • RNA-Puzzles
Abstract

EN 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.

Date of online publication

24.11.2021

Pages (from - to)

250 - 262

DOI

10.1261/rna.078685.121

URL

https://rnajournal.cshlp.org/content/28/2/250

License type

CC BY-NC (attribution - noncommercial)

Open Access Mode

czasopismo hybrydowe

Open Access Text Version

final published version

Date of Open Access to the publication

in press

Points of MNiSW / journal

140.0

Impact Factor

4.942 [List 2020]

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