Department of Mathematics, University of Campinas, Campinas, Brazil.
Department of Applied Mathematics, University of Campinas, Campinas, Brazil.
J Comput Chem. 2022 Feb 15;43(5):349-358. doi: 10.1002/jcc.26796. Epub 2021 Dec 14.
Due to the role of loops in protein function, loop modeling is an important problem in computational biology. We present a new approach to loop modeling based on a combinatorial version of distance geometry, where the search space of the associated problem is represented by a binary tree and a branch-and-prune method is defined to explore it, following an atomic ordering previously given. This ordering is used to calculate the coordinates of atoms from the positions of its predecessors. In addition to the theoretical development, computational results are presented to illustrate the advantage of the proposed method, compared with another approach of the literature. Our algorithm is freely available at https://github.com/michaelsouza/bpl.
由于环在蛋白质功能中的作用，环建模是计算生物学中的一个重要问题。我们提出了一种基于距离几何组合版本的新的环建模方法，其中相关问题的搜索空间由二叉树表示，并定义了分支定界方法来进行探索，遵循之前给定的原子顺序。这种排序用于根据其前导位置计算原子的坐标。除了理论发展，还给出了计算结果，以说明与文献中的另一种方法相比，所提出方法的优势。我们的算法可在 https://github.com/michaelsouza/bpl 上免费获得。
