Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.
Photobiology
Photochemistry
Python package
QM/MM
Rhodopsins
Journal
Topics in current chemistry (Cham)
ISSN: 2364-8961
Titre abrégé: Top Curr Chem (Cham)
Pays: Switzerland
ID NLM: 101691301
Informations de publication
Date de publication:
15 Mar 2022
15 Mar 2022
Historique:
received:
03
12
2021
accepted:
29
01
2022
entrez:
15
3
2022
pubmed:
16
3
2022
medline:
18
3
2022
Statut:
epublish
Résumé
In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.
Identifiants
pubmed: 35291019
doi: 10.1007/s41061-022-00374-w
pii: 10.1007/s41061-022-00374-w
pmc: PMC8924150
doi:
Substances chimiques
Rhodopsin
9009-81-8
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
21Subventions
Organisme : NIGMS NIH HHS
ID : R15 GM126627
Pays : United States
Organisme : Ministero dell'Istruzione, dell'Università e della Ricerca
ID : Rita Levi Montalcini grant, 2021-2024
Organisme : NIH HHS
ID : 1R15GM126627 01
Pays : United States
Organisme : National Science Foundation
ID : CHE-CLP-1710191
Informations de copyright
© 2022. The Author(s).
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