This article introduces Web-ARM, a specialized, on-line available, tool designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows to rapidly build models of rhodopsins with a documented quality and to predict trends in UV-Vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152], and as such necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.

Pedraza-González, L., Marín, M.D.C., Jorge, A.N., Ruck, T.D., Yang, X., Valentini, A., et al. (2020). Web-ARM: a web-based interface for the automatic construction of QM/MM models of rhodopsins. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 60(3), 1481-1493 [10.1021/acs.jcim.9b00615].

Web-ARM: a web-based interface for the automatic construction of QM/MM models of rhodopsins

Marín, María Del Carmen;Olivucci, Massimo
;
De Vico, Luca
2020-01-01

Abstract

This article introduces Web-ARM, a specialized, on-line available, tool designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows to rapidly build models of rhodopsins with a documented quality and to predict trends in UV-Vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152], and as such necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.
2020
Pedraza-González, L., Marín, M.D.C., Jorge, A.N., Ruck, T.D., Yang, X., Valentini, A., et al. (2020). Web-ARM: a web-based interface for the automatic construction of QM/MM models of rhodopsins. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 60(3), 1481-1493 [10.1021/acs.jcim.9b00615].
File in questo prodotto:
File Dimensione Formato  
acs.jcim.9b00615.pdf

non disponibili

Descrizione: Articolo
Tipologia: PDF editoriale
Licenza: NON PUBBLICO - Accesso privato/ristretto
Dimensione 6.67 MB
Formato Adobe PDF
6.67 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11365/1092074