A MULTISTAGE APPROACH TO PROTEIN-PROTEIN DOCKING

傅里叶相关技术对于对接边界非常有效 使用表面测量的蛋白质构象(即共结晶) 以互补性为目标函数。然而，当对接未绑定时(即， 独立结晶)构象，该方法产生大量的 假阳性的可能性(即分数高但RMSD大的构象)。这个 该建议的主要目标是将后处理步骤添加到傅里叶变换 对接算法，以消除所有误报。后处理将 包括刚体过滤器以减少候选结构的数量， 灵活的过滤器，可消除所有远离原生构象的构象(使用RMSD 超过10A)，以及灵活的对接算法来优化剩余的几个。这个 过滤和细化步骤利用不断变化的贡献， 静电学、去溶解和分子力学在不同的 蛋白质结合和对接的两个阶段。刚体分析 是基于静电和去溶相互作用的映射 遇到复合体中的蛋白质；即在广泛的表面接触之前 已经成立了。这些相互作用对结构的敏感性要低得多 扰动比表面互补性的度量更大，并提供了 有用的评分功能。然而，由于侧链的不同， 束缚态和非束缚态之间的构象，在 刚体分析，判别力不完美，不能消除 都是假阳性。包含分子力学和解释 灵活性带来了显著的改善。特别是，在广泛的 分子力学最小化的结构，范德华之和， 静电和溶剂化/熵能项不仅区分 在所有被研究的系统中，来自诱饵的近天然构象，但也提供了 近本土结构的排名相对较好。这些初步结果 支持中心假设，即所有假阳性都可以在 保持和改善良好的对接构象。网络的效率 通过以下预处理步骤进一步增加整个对接算法 要么尝试改善表面侧链的构象，要么 引入非均匀高斯模糊，以避免虚假重叠。 一种将傅里叶对接程序与POST-AND相结合的自动程序 前处理步骤将在以下应用程序中提供强大的研究工具 目前不能通过计算方法来解决。

Fourier correlation techniques are very efficient for docking bound (i.e., co-crystallized) protein conformations using measures of surface complementarity as the target function. However, when docking unbound (i.e., independently crystallized) conformations, the method yields an enormous number of false positives (i.e., conformations with good score but large RMSD). The major goal of this proposal is to add post-processing steps to the Fourier docking algorithm in order to remove all false positives. Post-processing will include a rigid-body filter to reduce the number of candidate structures, a flexible filter that eliminates all far-from-native conformations (with RMSDs over 10 A), and a flexible docking algorithm to refine the remaining few. The filtering and refinement steps utilize the changing contributions that electrostatics, desolvation, and molecular mechanics exhibit at the different stages of both protein-protein association and docking. The rigid body analysis is based on the mapping of electrostatic and desolvation interactions between proteins in encounter complexes; i.e., before extensive surface contacts are established. These interactions are much less sensitive to structural perturbations than the measures of surface complementarity, and provide a useful scoring function. However, due to the differences in side chain conformations between bound and unbound states, within the framework of the rigid body analysis, the discrimination is not perfect, and cannot eliminate all false positives. Inclusion of molecular mechanics and accounting for flexibility yield dramatic improvement. In particular, after extensive molecular mechanics minimization of the structures, the sum of van der Waals, electrostatic, and solvation/entropic energy terms, not only discriminates the near-native conformations from decoys in all systems studied, but also provides a relatively good ranking of near-native structures. These preliminary results support the central hypothesis that all false positives can be removed while retaining and improving the good docked conformations. The efficiency of the entire docking algorithm is further increased by pre-processing steps that either attempt to improve the conformations of surface side chains, or introduce a nonuniform Gaussian blurring in order to avoid spurious overlaps. An automatic procedure combining Fourier docking programs with the post- and pre-processing steps will provide a powerful research tool in applications that currently cannot be addressed by computational methods.