Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F62156489%3A43210%2F19%3A43915691" target="_blank" >RIV/62156489:43210/19:43915691 - isvavai.cz</a>
Alternative codes found
RIV/00216305:26620/19:PU132593
Result on the web
<a href="https://doi.org/10.1016/j.bpj.2019.04.017" target="_blank" >https://doi.org/10.1016/j.bpj.2019.04.017</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.bpj.2019.04.017" target="_blank" >10.1016/j.bpj.2019.04.017</a>
Alternative languages
Result language
angličtina
Original language name
Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins
Original language description
Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles)in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD)of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD)in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10610 - Biophysics
Result continuities
Project
<a href="/en/project/GA18-10251S" target="_blank" >GA18-10251S: Comprehensive insight into mechanisms of action and metabolism of tyrosine kinase inhibitors and a study of ways increasing their antitumor efficiency</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Biophysical Journal
ISSN
0006-3495
e-ISSN
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Volume of the periodical
116
Issue of the periodical within the volume
11
Country of publishing house
US - UNITED STATES
Number of pages
11
Pages from-to
2062-2072
UT code for WoS article
000470092800003
EID of the result in the Scopus database
2-s2.0-85065395420