Robert C H, Janin J
Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Bâtiment 34 -, Gif-sur-Yvette Cedex, 91198, France.
J Mol Biol. 1998 Nov 13;283(5):1037-47. doi: 10.1006/jmbi.1998.2152.
We derive a series of novel mean-field potentials from statistical analyses of protein-protein contact regions in crystal structures. These potentials are parameterized in terms of the number of contacts made by an atom in an interface region. Such an explicit number dependence avoids the pairwise assumption and is intrinsically softer than distance-based approaches. It appears well suited to protein-protein docking applications, for which detailed interface geometry is generally lacking. In tests including protein complex reconstitution and docking of independently determined protein structures, we show that a hydrophobic potential of this type performs remarkably well, identifying native-like complexes by their favourable potential energies and in several cases demonstrating a recognition energy gap of 4-8 kcal/mol according to the system.
我们通过对晶体结构中蛋白质-蛋白质接触区域的统计分析得出了一系列新的平均场势。这些势根据界面区域中一个原子形成的接触数进行参数化。这种明确的数量依赖性避免了成对假设，并且本质上比基于距离的方法更灵活。它似乎非常适合蛋白质-蛋白质对接应用，因为此类应用通常缺乏详细的界面几何信息。在包括蛋白质复合物重构和独立测定的蛋白质结构对接的测试中，我们表明这种类型的疏水势表现出色，通过其有利的势能识别出类似天然的复合物，并且在某些情况下，根据系统不同，展示出4-8千卡/摩尔的识别能隙。
