期刊
RNA
卷 28, 期 2, 页码 250-262出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.078685.121
关键词
stereochemistry; quality validation; RNA structure; 3D structure prediction; RNA-Puzzles
资金
- Polish National Science Center [2016/23/B/ST6/03931, 2019/35/B/ST6/03074, POIR.04.02.00-30-A004/16]
- Poznan University of Technology (SBAD), Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences
This paper analyzes the stereochemical quality of predicted RNA three-dimensional models and aims to improve RNA 3D structure modeling approaches by reducing deviations from standard bond lengths and angles, planarity, or chirality.
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.
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