AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes
AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes
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DOI：
10.1093/nar/gkaa356
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发表时间：
2020-07-02
影响因子：
14.9
通讯作者：
Wolynes, Peter G.
中科院分区：
文献类型：
--
作者：
Jin, Shikai;Contessoto, Vinicius G.;Wolynes, Peter G.
尽管蛋白质及其组装体的三维结构的求解数量激增，预测技术不断改进，但准确可靠地预测蛋白质及其组装体的三维结构仍然很困难。在这项研究中，一个免费和开放访问的Web服务器，AWSEM-Suite，其目标是预测单体蛋白质的三级结构序列进行了描述。服务器预测的基础模型是一个粗粒度的蛋白质力场，它源于神经网络思想，并使用能量景观理论进行了优化。采用物理驱动的潜力和知识为基础的局部结构偏置项，同源模板和协同进化的限制，AWSEM-Suite的加入大大提高了纯AWSEM结构预测的预测能力。从CASP 13实验中发布的独立评估指标来看，AWSEM-Suite被证明是一种相当准确的自由建模算法，在CASP 13的自由建模类别中排名第八。AWSEM-Suite服务器还具有用户友好界面的前端。AWSEM-Suite服务器是预测单体蛋白质三级结构的强大工具，在没有合适的结构模板时非常有用。尽管蛋白质及其组装体的三维结构数量激增，预测技术不断改进，但准确可靠地预测蛋白质及其组装体的三维结构仍然很困难。在这项研究中，一个免费和开放访问的Web服务器，AWSEM-Suite，其目标是预测单体蛋白质的三级结构序列进行了描述。服务器预测的基础模型是一个粗粒度的蛋白质力场，它源于神经网络思想，并使用能量景观理论进行了优化。采用物理驱动的潜力和知识为基础的局部结构偏置项，同源模板和协同进化的限制，AWSEM-Suite的加入大大提高了纯AWSEM结构预测的预测能力。从CASP 13实验中发布的独立评估指标来看，AWSEM-Suite被证明是一种相当准确的自由建模算法，在CASP 13的自由建模类别中排名第八。AWSEM-Suite服务器还具有用户友好界面的前端。AWSEM-Suite服务器是预测单体蛋白质三级结构的强大工具，在没有合适的结构模板时最有用。AWSEM-Suite服务器可以在https://awsem.rice.edu上免费获得。
The accurate and reliable prediction of the 3D structures of proteins and their assemblies remains difficult even though the number of solved structures soars and prediction techniques improve. In this study, a free and open access web server, AWSEM-Suite, whose goal is to predict monomeric protein tertiary structures from sequence is described. The model underlying the server's predictions is a coarse-grained protein force field which has its roots in neural network ideas that has been optimized using energy landscape theory. Employing physically motivated potentials and knowledge-based local structure biasing terms, the addition of homologous template and co-evolutionary restraints to AWSEM-Suite greatly improves the predictive power of pure AWSEM structure prediction. From the independent evaluation metrics released in the CASP13 experiment, AWSEM-Suite proves to be a reasonably accurate algorithm for free modeling, standing at the eighth position in the free modeling category of CASP13. The AWSEM-Suite server also features a front end with a user-friendly interface. The AWSEM-Suite server is a powerful tool for predicting monomeric protein tertiary structures that is most useful when a suitable structure template is not available.The accurate and reliable prediction of the 3D structures of proteins and their assemblies remains difficult even though the number of solved structures soars and prediction techniques improve. In this study, a free and open access web server, AWSEM-Suite, whose goal is to predict monomeric protein tertiary structures from sequence is described. The model underlying the server's predictions is a coarse-grained protein force field which has its roots in neural network ideas that has been optimized using energy landscape theory. Employing physically motivated potentials and knowledge-based local structure biasing terms, the addition of homologous template and co-evolutionary restraints to AWSEM-Suite greatly improves the predictive power of pure AWSEM structure prediction. From the independent evaluation metrics released in the CASP13 experiment, AWSEM-Suite proves to be a reasonably accurate algorithm for free modeling, standing at the eighth position in the free modeling category of CASP13. The AWSEM-Suite server also features a front end with a user-friendly interface. The AWSEM-Suite server is a powerful tool for predicting monomeric protein tertiary structures that is most useful when a suitable structure template is not available. The AWSEM-Suite server is freely available at: https://awsem.rice.edu.