MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.
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DOI：
10.1002/prot.22797
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发表时间：
2010-11-15
影响因子：
2.9
通讯作者：
Zou, Xiaoqin
中科院分区：
文献类型：
--
作者：
Huang, Sheng-You;Zou, Xiaoqin
一种分层方法已被开发用于蛋白质 - 蛋白质对接。在第一步中，使用基于快速傅里叶变换（FFT）的对接算法对所有假定的结合模式进行全局采样，其中蛋白质由简化模型表示，即蛋白质表面的每个侧链由其质心表示。与使用全原子模型的常规FFT对接相比，使用简化模型的FFT对接方法预计会产生更多的命中结果，因为它允许更大的侧链灵活性。接下来，通过迭代推导的基于知识的评分函数ITScorePP，并使用集成对接算法考虑主链/环的灵活性，对筛选出的结合模式（通常数千个）进行优化。ITScorePP的距离相关势能是通过基于物理的迭代方法提取的，这避免了基于知识的方法中长期存在的参考态问题。通过这种分层协议，我们参与了针对11个目标（T32 - T42）的第15 - 19轮CAPRI实验。在预测实验中，我们对六个目标获得了正确的结合模式：三个具有高精度（T40的两种不同结合模式、T41和T42），两个具有中等精度（T34和T37），一个是可接受的（T32）。在评分实验中，在由CAPRI预测小组提交的包含至少一种可接受模式的七个目标复合物中，我们对四个目标获得了正确的结合模式：三个具有高精度（T37、T40和T41），一个具有中等精度（T34），这表明ITScorePP具有良好的准确性和稳健性。
A hierarchical approach has been developed for protein-protein docking. In the first step, a Fast Fourier Transform (FFT)-based docking algorithm is used to globally sample all putative binding modes, in which the protein is represented by a reduced model, that is, each side chain on the protein surface is represented by its center of mass. Compared to conventional FFT docking with all-atom models, the FFT docking method with a reduced model is expected to generate more hits because it allows larger side-chain flexibility. Next, the filtered binding modes (normally several thousands) are refined by an iteratively derived knowledge-based scoring function ITScorePP and by considering backbone/loop flexibility using an ensemble docking algorithm. The distance-dependent potentials of ITScorePP were extracted by a physics-based iterative method, which circumvents the long-standing reference state problem in the knowledge-based approaches. With this hierarchical protocol, we have participated in the CAPRI experiments for Rounds 15–19 of 11 targets (T32-T42). In the predictor experiments, we achieved correct binding modes for six targets: three are with high accuracy (T40 for both distinct binding modes, T41, and T42), two are with medium accuracy (T34 and T37), and one is acceptable (T32). In the scorer experiments, of the seven target complexes that contain at least one acceptable mode submitted by the CAPRI predictor groups, we obtained correct binding modes for four targets: three are with high accuracy (T37, T40, and T41) and one is with medium accuracy (T34), suggesting good accuracy and robustness of ITScorePP.
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影响因子：
5.6
作者：
Gabb, HA;Jackson, RM;Sternberg, MJE
通讯作者：
Sternberg, MJE
DOI：
10.1002/prot.10390
发表时间：
2003-07-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Chen, R;Mintseris, J;Weng, ZP
通讯作者：
Weng, ZP
影响因子：
64.8
作者：
BLOW, DM;JANIN, J;SWEET, RM
通讯作者：
SWEET, RM
影响因子：
8
作者：
Heifetz, A;Katchalski-Katzir, E;Eisenstein, M
通讯作者：
Eisenstein, M
影响因子：
4.8
作者：
Forouhar, F;Hussain, M;Hunt, JF
通讯作者：
Hunt, JF