Structure modeling of RNA using sparse NMR constraints.
Structure modeling of RNA using sparse NMR constraints.
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DOI：
10.1093/nar/gkx1058
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发表时间：
2017-12-15
影响因子：
14.9
通讯作者：
Dokholyan NV
中科院分区：
文献类型：
--
作者：
Williams B 2nd;Zhao B;Tandon A;Ding F;Weeks KM;Zhang Q;Dokholyan NV
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs.
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影响因子：
2.7
作者：
Grishaev A;Ying J;Canny MD;Pardi A;Bax A
通讯作者：
Bax A
DOI：
10.1016/s1359-0278(98)00072-8
发表时间：
1998-01-01
期刊：
FOLDING & DESIGN
影响因子：
--
作者：
Dokholyan, NV;Buldyrev, SV;Shakhnovich, EI
通讯作者：
Shakhnovich, EI
影响因子：
4.5
作者：
Ding, Feng;Sharma, Shantanu;Dokholyan, Nikolay V.
通讯作者：
Dokholyan, Nikolay V.
影响因子：
6.8
作者：
Laing, Christian;Schlick, Tamar
通讯作者：
Schlick, Tamar
影响因子：
5.6
作者：
Kim, Nak-Kyoon;Zhang, Qa;Feigon, Juli
通讯作者：
Feigon, Juli