Computational reconstruction of atomistic protein structures from coarse-grained models

• Main Authors: Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik
• Format: Article
• Language: English
• Published: Elsevier 2020-01-01
• Series: Computational and Structural Biotechnology Journal
• Subjects: Protein reconstruction; Structure prediction; Coarse-grained modeling; Structure refinement; Protein modeling
• Online Access: http://www.sciencedirect.com/science/article/pii/S2001037019305537

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.