Computational reconstruction of atomistic protein structures from coarse-grained models

Bibliographic Details
Title:	Computational reconstruction of atomistic protein structures from coarse-grained models
Authors:	Badaczewska-Dawid, Aleksandra E., Kolinski, Andrzej, Kmiecik, Sebastian
Publisher Information:	Research Network of Computational and Structural Biotechnology
Publication Year:	2019
Collection:	PubMed Central (PMC)
Subject Terms:	Review Article
Description:	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.
Document Type:	text
Language:	English
Relation:	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961067/; http://dx.doi.org/10.1016/j.csbj.2019.12.007
DOI:	10.1016/j.csbj.2019.12.007
Availability:	https://doi.org/10.1016/j.csbj.2019.12.007 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961067/
Rights:	© 2019 The Authors ; http://creativecommons.org/licenses/by-nc-nd/4.0/ ; This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Accession Number:	edsbas.DC122A60
Database:	BASE

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