Badaczewska-Dawid Aleksandra E, Kolinski Andrzej, Kmiecik Sebastian
Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
Comput Struct Biotechnol J. 2019 Dec 26;18:162-176. doi: 10.1016/j.csbj.2019.12.007. eCollection 2020.
Three-dimensional protein structures, whether determined experimentally or theoretically, are often too low resolution. In this mini-review, we outline the computational methods for protein structure reconstruction from incomplete coarse-grained to all atomistic models. Typical reconstruction schemes can be divided into four major steps. Usually, the first step is reconstruction of the protein backbone chain starting from the C-alpha trace. This is followed by side-chains rebuilding based on protein backbone geometry. Subsequently, hydrogen atoms can be reconstructed. Finally, the resulting all-atom models may require structure optimization. Many methods are available to perform each of these tasks. We discuss the available tools and their potential applications in integrative modeling pipelines that can transfer coarse-grained information from computational predictions, or experiment, to all atomistic structures.
三维蛋白质结构，无论是通过实验还是理论确定的，其分辨率往往都很低。在这篇小型综述中，我们概述了从不完全的粗粒度模型到全原子模型进行蛋白质结构重建的计算方法。典型的重建方案可分为四个主要步骤。通常，第一步是从Cα迹线开始重建蛋白质主链。接下来是基于蛋白质主链几何结构重建侧链。随后，可以重建氢原子。最后，得到的全原子模型可能需要进行结构优化。有许多方法可用于执行这些任务中的每一项。我们讨论了可用的工具及其在整合建模流程中的潜在应用，这些流程可以将粗粒度信息从计算预测或实验转移到全原子结构。
