A novel method for scoring of docked protein complexes using predicted protein-protein binding sites.
A novel method for scoring of docked protein complexes using predicted protein-protein binding sites.
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一种使用预测的蛋白质-蛋白质结合位点对对接蛋白质复合物进行评分的新方法。
DOI：
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发表时间：
2004
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通讯作者：
G. Schreiber
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作者：
K. Gottschalk;Hani Neuvirth;G. Schreiber
对接算法产生蛋白质-蛋白质复合物的许多可能结构。在大多数情况下，它们中的一些类似于r.m.s.d.中的正确结构。<3 A。对接领域的一个主要挑战是从这个池中提取正确的结构，即所谓的“评分”。在这里，我们引入了一个新的评分函数，它区分了许多错误和少数真正的构象。评分函数基于测量两个对接蛋白在预测结合界面处的拟合紧密度。使用最近开发的计算机算法ProMate的结合界面的位置被确定。新的评分函数不依赖于能量考虑。因此，它可以容忍接口的低分辨率描述。得分与均方根差呈线性关系。相对于“真实结构”，在大多数评估的情况下都可以找到。该功能进行了测试的对接结果的21复合物在其未结合的形式。在77%的检查病例中发现成功，将成功定义为p值优于0.1的“真实”结果。
Docking algorithms produce many possible structures of a protein-protein complex. In most cases some of them resemble the correct structure within an r.m.s.d. of <3 A. A major challenge in the field of docking is to extract the correct structure out of this pool, the so-called 'scoring'. Here, we introduce a new scoring function, which discriminates between the many wrong and few true conformations. The scoring function is based on measuring the tightness of fit of the two docked proteins at a predicted binding interface. The location of the binding interface is identified using the recently developed computer algorithm ProMate. The new scoring function does not rely on energy considerations. It is therefore tolerant to low-resolution descriptions of the interface. A linear relation between the score and the r.m.s.d. relative to the 'true structure' is found in most of the cases evaluated. The function was tested on the docking results of 21 complexes in their unbound form. It was found to be successful in 77% of the examined cases, defining success as scoring a 'true' result with a p value of better than 0.1.