期刊
NUCLEIC ACIDS RESEARCH
卷 48, 期 2, 页码 576-588出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkz1108
关键词
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资金
- Polish National Science Centre [NCN] [2015/17/N/NZ2/03360, 2016/23/B/ST6/03931, 2016/23/N/ST6/03779, 2017/26/A/NZ 1/01083]
- Foundation for Polish Science - European Union under the European Regional Development Fund [MAB/20172]
- Institute of Computing Science, Poznan University of Technology [09/91/SBAD/0681]
- Single Cell Gene Expression Atlas grant from the Wellcome Trust [108437/Z/15/Z]
- Shanghai Fourth People's Hospital
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.
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