通过利用多维能量漏斗进行具有降低势的蛋白质-蛋白质对接。
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.
作者信息
Paschalidis Ioannis Ch, Shen Yang, Vakili Pirooz, Vajda Sandor
机构信息
Center for Information & Systems Eng., and Dept. of Manufacturing Eng., Boston University, Blookline, MA 2446, USA.
出版信息
Conf Proc IEEE Eng Med Biol Soc. 2006;2006:5330-3. doi: 10.1109/IEMBS.2006.260790.
We propose a new computational approach for protein docking exploiting energy funnels in the 6-dimensional space of translations and rotations of the ligand with respect to the receptor. Our approach consists of a series of translational and orientational moves of the ligand towards the receptor. Each move is performed using a global optimization method we have developed - the semi-definite underestimation (SDU) method - which can exploit a funnel-like energy function. We compared our approach with Monte Carlo on a set of 10 protein complexes using two residue-level potentials. To achieve the same level of performance (produce a near-native < or =3 A RMSD complex) our approach reduces energy evaluations by more than a factor of two, on average.
我们提出了一种新的蛋白质对接计算方法，该方法利用配体相对于受体在平移和旋转的六维空间中的能量漏斗。我们的方法包括一系列配体向受体的平移和定向移动。每次移动都使用我们开发的一种全局优化方法——半定低估（SDU）方法来执行，该方法可以利用类似漏斗的能量函数。我们使用两种残基水平的势，在一组10个蛋白质复合物上，将我们的方法与蒙特卡罗方法进行了比较。为了达到相同的性能水平（产生一个接近天然结构的、RMSD小于或等于3埃的复合物），我们的方法平均减少了两倍多的能量评估次数。
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