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Unveiling the Details of the Phosphoryl Transfer Mechanism in Cyclin-Dependent Kinases: Insights from QM/MM Calculations.
(2016)
Protein kinases have become the second most important therapeutic target after G-protein-coupled receptors, therefore a complete understanding of the reaction mechanisms taking place in this protein family is desired. CDKs ...
GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
(American Chemical Society, 2014-02)
The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density ...
Estudo da dinâmica de solvatação de peptídeos por QM/MMStudy of the solvation dynamic of peptides by QM/MM
(Universidade Estadual Paulista (Unesp), 2016)
Simulating DNA chip design using all-electronic graphene-based substrates
(2019-01-01)
In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes ...
Unveiling the tartrazine binding mode with ds–DNA by UV–visible spectroscopy, electrochemical, and QM/MM methods
(2023-05)
Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the ...
Estudo da dinâmica de solvatação de peptídeos por QM/MM
(Universidade Estadual Paulista (Unesp), 2015-12-11)
Trabalhos experimentais e teóricos desenvolvidos nos últimos anos evidenciaram a capacidade de alcoóis e polialcoóis em mudar características energéticas em proteínas. No entanto, o mecanismo responsável por esse efeito ...
Chemical reactivity and spectroscopy explored from QM/MM molecular dynamics simulations using the LIO code
(Frontiers Media SA, 2018-03)
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with ...