Three new strategies for sampling the conformation space accessible to a series of structurally diverse, flexible molecules are defined and compared to samples obtained using a fixed-grid torsion angle sampling strategy. A set of 28 potent inhibitors of angiotensin converting enzyme selected by Mayer et al. [J. Comput.-Aided Mol. Design, 1 (1987) 3] and the unrestricted active-site model proposed by Waller et al. [to be published] are used to produce a realistic experimental setting. We modified our Constrained Search algorithm [Dammkoehler et al., J. Comput.-Aided Mol. Design, 3 (1989) 3] to support these new sampling strategies, performing a series of 64 simulations (search experiments) and generating a large set of sterically allowed conformations. In each experiment, we systematically vary the internal torsion angles in each molecule using one of the sampling strategies. The common orientations of preselected functional groups thought to represent those dominating the interaction with the enzyme and presented by the set of molecules are classified and recorded for each experiment. Pairwise distances between groups are used to characterize the geometry of the common orientations. The results of each experiment, represented by a set of distance values, are compared and combined to evaluate the completeness of the conformational sampling. While no pure strategy or single search experiment was found to be adequate to fully explore the set of common sterically allowed conformations, a new sampling technique, called adaptive radial sampling, is shown to be significantly more complete than the commonly used fixed grid sampling.

译文

定义了三种新的策略来采样一系列结构多样的柔性分子可访问的构象空间,并将其与使用固定网格扭转角采样策略获得的样品进行比较。Mayer等人 [J. Comput-辅助Mol. Design,1 (1987) 3] 选择的一组28种有效的血管紧张素转化酶抑制剂和Waller等人 [将要发表] 提出的不受限制的活性位点模型用于产生现实的实验环境。我们修改了约束搜索算法 [Dammkoehler等人,J. Comput.-辅助Mol. Design,3 (1989) 3] 以支持这些新的采样策略,执行一系列64个模拟 (搜索实验) 并生成大量空间允许的构象。在每个实验中,我们使用一种采样策略系统地改变每个分子的内部扭转角。对于每个实验,对预选官能团的共同方向进行了分类和记录,这些官能团被认为代表了与酶相互作用的那些,并由一组分子呈现。组之间的成对距离用于表征公共方向的几何形状。将每个实验的结果 (由一组距离值表示) 进行比较和组合,以评估构象采样的完整性。虽然没有发现纯策略或单一搜索实验足以充分探索常见的空间允许构象集,但一种称为自适应径向采样的新采样技术比常用的固定网格采样要完整得多。

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