Zheng Q, Rosenfeld R, Vajda S, DeLisi C
Department of Biomedical Engineering, College of Engineering, Boston University, Massachusetts 02215.
Protein Sci. 1993 Aug;2(8):1242-8. doi: 10.1002/pro.5560020806.
We recently developed a rapid loop closure algorithm in which bond lengths are scaled to constrain the ends of a segment to match a known distance and then gradually relaxed to their standard values, with boundary constraints maintained. Although the algorithm predicted the Zif286 zinc-finger loop to within approximately 2 A, it had a serious limitation that made its more general use tentative: it omitted the atomic environment of the loop. Here we report an extension of the algorithm to take into account the protein environment surrounding a given loop from the outset of the conformational search and show that it predicts structure with an efficiency and accuracy that could not be achieved without continuous environmental inclusion. The algorithm should be widely applicable to structure determination when complete experimental information is unavailable.
我们最近开发了一种快速闭环算法，其中键长被缩放以约束片段的末端，使其与已知距离匹配，然后逐渐松弛到其标准值，同时保持边界约束。尽管该算法将Zif286锌指环预测在约2埃的范围内，但它有一个严重的局限性，使得其更广泛的应用受到限制：它忽略了环的原子环境。在此，我们报告了该算法的扩展，以便从构象搜索一开始就考虑给定环周围的蛋白质环境，并表明它预测结构的效率和准确性是在不持续考虑环境的情况下无法实现的。当没有完整的实验信息时，该算法应广泛适用于结构测定。
