ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts.
ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts.
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DOI：
10.1093/nar/gkab300
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发表时间：
2021-07-02
影响因子：
14.9
通讯作者：
McGuffin LJ
中科院分区：
文献类型：
--
作者：
Adiyaman R;McGuffin LJ
ReFOLD3的独特之处在于它应用了渐进约束，通过局部模型质量估计和接触预测计算得出，这些预测用于指导理论3D蛋白质模型向自然结构的精细化。ReFOLD3通过使用迭代改进协议来修复不正确的残基接触和局部错误，包括异常键和角度，从而提高了性能，这些错误是通过我们领先的ModFOLD8模型质量评估方法在提交的模型中确定的。经过改进后，可能对提交的模型产生的改进得到了ModFOLD8的认可，该公司同时生成全球和本地质量估计。在CASP14预测季节(2020年5月至8月)，我们使用ReFOLD3协议对数百个3D模型进行了细化，包括细化和主要三级结构预测类别。我们小组在精细化类别中提高了众多起步车型的全球和本地质量分数，根据官方评估，我们在该类别中排名前十。作为CASP Commons新冠肺炎倡议的一部分，ReFOLD3协议也被用于改进SARS-CoV-2目标，我们提供了相当多的前10个模型。ReFOLD3Web服务器可以在https://www.reading.ac.uk/bioinf/ReFOLD/.上免费获得使用ReFOLD3优化3D模型。
ReFOLD3 is unique in its application of gradual restraints, calculated from local model quality estimates and contact predictions, which are used to guide the refinement of theoretical 3D protein models towards the native structures. ReFOLD3 achieves improved performance by using an iterative refinement protocol to fix incorrect residue contacts and local errors, including unusual bonds and angles, which are identified in the submitted models by our leading ModFOLD8 model quality assessment method. Following refinement, the likely resulting improvements to the submitted models are recognized by ModFOLD8, which produces both global and local quality estimates. During the CASP14 prediction season (May–Aug 2020), we used the ReFOLD3 protocol to refine hundreds of 3D models, for both the refinement and the main tertiary structure prediction categories. Our group improved the global and local quality scores for numerous starting models in the refinement category, where we ranked in the top 10 according to the official assessment. The ReFOLD3 protocol was also used for the refinement of the SARS-CoV-2 targets as a part of the CASP Commons COVID-19 initiative, and we provided a significant number of the top 10 models. The ReFOLD3 web server is freely available at https://www.reading.ac.uk/bioinf/ReFOLD/. Refinement of a 3D model using ReFOLD3.
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影响因子：
2.9
作者：
Haas J;Barbato A;Behringer D;Studer G;Roth S;Bertoni M;Mostaguir K;Gumienny R;Schwede T
通讯作者：
Schwede T
影响因子：
5.5
作者：
Goetz, Andreas W.;Williamson, Mark J.;Xu, Dong;Poole, Duncan;Le Grand, Scott;Walker, Ross C.
通讯作者：
Walker, Ross C.
影响因子：
3.7
作者：
Bhattacharya D;Cheng J
通讯作者：
Cheng J
通过分子动力学系综的结构选择和平均来细化蛋白质结构。
影响因子：
5.5
作者：
Mirjalili, Vahid;Feig, Michael
通讯作者：
Feig, Michael
DOI：
10.1073/pnas.0906514106
发表时间：
2009-08-18
影响因子：
11.1
作者：
Kliger, Yossef;Levy, Ofer;Borukhov, Itamar
通讯作者：
Borukhov, Itamar