Structure prediction for CASP8 with all-atom refinement using Rosetta.

Raman S; Vernon R; Thompson

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Structure prediction for CASP8 with all-atom refinement using Rosetta.

机译：使用Rosetta进行全原子精修的CASP8的结构预测。

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We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.

机译：我们描述了使用Rosetta结构预测方法进行蛋白质结构预测技术的第八次关键评估的预测。几乎所有目标均进行了激进采样和全原子细化。使用对齐方法的组合从一系列模板生成初始模型，然后对模型进行Rosetta所有原子精修。对于具有容易识别模板的64个域，最佳提交模型优于针对蛋白质数据库中最佳模板的最佳比对24例，并且优于43例的最佳起始模型。对于仅检测到与已知结构的蛋白质具有非常远的序列关系的13个靶标，使用Rosetta de novo结构预测方法进行建模，然后进行全原子精炼;在某些情况下，提交的模型要优于基于可用模板的模型。在12个优化挑战中，提交得最好的模型在7个案例中比初始模型有所改进。这些对基于初始模板的模型的改进和改进测试证明了Rosetta结构改进在提高模型准确性中的作用。

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《Proteins: Structure, Function, and Genetics》 |2009年第9期|共11页
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Raman S; Vernon R; Thompson;
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1. Structure prediction for CASP8 with all-atom refinement using Rosetta. [J] . Raman S, Vernon R, Thompson Proteins: Structure, Function, and Genetics . 2009,第Suppla9期

机译：使用Rosetta进行全原子精修的CASP8的结构预测。
2. Protein structure prediction by all-atom free-energy refinement [J] . Abhinav Verma, Wolfgang Wenzel BMC Structural Biology . 2007,第1期

机译：通过全原子自由能精炼预测蛋白质结构
3. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. [J] . Das R, Qian B, Raman S, Proteins: Structure, Function, and Genetics . 2007,第Suppla8期

机译：使用Rosetta @ home进行的全原子细化，对CASP7目标的结构预测。
4. DEVELOPMENT OF A NEW META-SCORE FOR PROTEINSTRUCTURE PREDICTION FROM SEVEN ALL-ATOM DISTANCEDEPENDENT POTENTIALS USING SUPPORT VECTOR REGRESSION [C] . MATSUYUKI SHIROTA, TAKASHI ISHIDA, KENGO KINOSHITA International Conference on Genome Informatics . 2009

机译：从七个全原子距离依赖潜力使用支持向量回归开发蛋白质结构预测的新荟萃评分
5. Theoretical studies of proteins and protein-ligand complexes: Part I. Toward the development of an efficient all-atom implicit-solvent model for use in protein structure prediction. Part II. Molecular dynamics of studies of trypsin-ligand complexes. [D] . Guvench, Olgun. 2005

机译：蛋白质和蛋白质-配体配合物的理论研究：第一部分。建立用于蛋白质结构预测的有效全原子隐式溶剂模型。第二部分胰蛋白酶-配体复合物的分子动力学研究。
6. Structure prediction for CASP8 with all-atom refinement using Rosetta [O] . Srivatsan Raman, Robert Vernon, James Thompson, -1

机译：使用Rosetta进行全原子精修的CASP8的结构预测
7. Structure prediction for CASP8 with all-atom refinement using Rosetta [O] . Srivatsan Raman, Robert Vernon, James Thompson, 2009

机译：使用Rosetta与全原子改进的Casp8结构预测

Structure prediction for CASP8 with all-atom refinement using Rosetta.

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