Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK.
Int J Mol Sci. 2010 Sep 28;11(10):3623-48. doi: 10.3390/ijms11103623.
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.
本文从理论和实践两方面研究了在蛋白质-蛋白质对接中使用本征模的情况。在一个大型测试集上计算了本征模捕捉无键合到键合构象变化的能力的上限，特别关注了结合界面，这是从计算结合能的残基子集。此外，还提出了 SwarmDock 算法，以证明将构象变化建模为本征模的线性组合是蛋白质-蛋白质对接中建模柔性的有效方法。
