Collective Variable for Metadynamics Derived From AlphaFold Output
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F22%3A43924443" target="_blank" >RIV/60461373:22330/22:43924443 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14610/22:00129134
Result on the web
<a href="https://www.frontiersin.org/articles/10.3389/fmolb.2022.878133/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fmolb.2022.878133/full</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3389/fmolb.2022.878133" target="_blank" >10.3389/fmolb.2022.878133</a>
Alternative languages
Result language
angličtina
Original language name
Collective Variable for Metadynamics Derived From AlphaFold Output
Original language description
AlphaFold is a neural network–based tool for the prediction of 3D structures of proteins. In CASP14, a blind structure prediction challenge, it performed significantly better than other competitors, making it the best available structure prediction tool. One of the outputs of AlphaFold is the probability profile of residue–residue distances. This makes it possible to score any conformation of the studied protein to express its compliance with the AlphaFold model. Here, we show how this score can be used to drive protein folding simulation by metadynamics and parallel tempering metadynamics. Using parallel tempering metadynamics, we simulated the folding of a mini-protein Trp-cage and β hairpin and predicted their folding equilibria. We observe the potential of the AlphaFold-based collective variable in applications beyond structure prediction, such as in structure refinement or prediction of the outcome of a mutation. Copyright © 2022 Spiwok, Kurečka and Křenek.
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
10608 - Biochemistry and molecular biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Frontiers in Molecular Biosciences
ISSN
2296-889X
e-ISSN
2296-889X
Volume of the periodical
9
Issue of the periodical within the volume
Neuveden
Country of publishing house
CH - SWITZERLAND
Number of pages
10
Pages from-to
"878133_1"-"878133_10"
UT code for WoS article
000816408600001
EID of the result in the Scopus database
2-s2.0-85133463409