Protein structure prediction using Rosetta in CASP12.
Protein structure prediction using Rosetta in CASP12.
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作者：
Ovchinnikov S;Park H;Kim DE;DiMaio F;Baker D
我们描述了几个值得注意的方面，我们的结构预测使用Rosetta在CASP 12中的自由建模（FM）和细化（TR）类别。首先，我们之前已经为大多数缺乏实验确定结构的大型蛋白质家族生成（并发布）模型，使用Rosetta由基于共同进化的接触预测指导，对于几个目标，这些模型被证明比任何已知的晶体结构都更好的比较建模起点-我们的模型数据库因此开始实现原始蛋白质结构倡议的目标之一。其次，虽然我们的“人类”小组只是提交了大多数目标的ROBETTA模型，但对于六个目标，专家干预大大改善了预测;最大的改进是T0886，我们正确地解析了预测接触图指导的两个不连续结构域，以准确地识别相同折叠的结构同源物。第三，罗塞塔所有原子细化后，MD模拟导致一致的，但小的改进时，启动模型接近原生结构，和较大的，但不一致的改进时，启动模型更远。
We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we had previously generated (and published) models for most large protein families lacking experimentally determined structures using Rosetta guided by co-evolution based contact predictions, and for several targets these models proved better starting points for comparative modeling than any known crystal structure—our model database thus starts to fulfill one of the goals of the original protein structure initiative. Second, while our “human” group simply submitted ROBETTA models for most targets, for six targets expert intervention improved predictions considerably; the largest improvement was for T0886 where we correctly parsed two discontinuous domains guided by predicted contact maps to accurately identify a structural homolog of the same fold. Third, Rosetta all atom refinement followed by MD simulations led to consistent but small improvements when starting models were close to the native structure, and larger but less consistent improvements when starting models were further away.
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通讯作者：
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DOI：
10.1073/pnas.1515561112
发表时间：
2015-09-22
影响因子：
11.1
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通讯作者：
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