[HTML][HTML] The chemistry of snake venom and its medicinal potential

AL Oliveira, MF Viegas, SL da Silva… - Nature Reviews …, 2022 - nature.com
The fascination and fear of snakes dates back to time immemorial, with the first scientific
treatise on snakebite envenoming, the Brooklyn Medical Papyrus, dating from ancient Egypt …

The quantum chemical cluster approach in biocatalysis

X Sheng, F Himo - Accounts of Chemical Research, 2023 - ACS Publications
Conspectus The quantum chemical cluster approach has been used for modeling enzyme
active sites and reaction mechanisms for more than two decades. In this methodology, a …

[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD

JC Phillips, DJ Hardy, JDC Maia, JE Stone… - The Journal of …, 2020 - pubs.aip.org
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

Reaction mechanism of the PET degrading enzyme PETase studied with DFT/MM molecular dynamics simulations

C Jerves, RPP Neves, MJ Ramos, S da Silva… - ACS …, 2021 - ACS Publications
Polyethylene terephthalate (PET) has been widely used to make disposable bottles, among
others, leading to massive PET waste accumulation in the environment. The discovery of the …

Methods for exploring reaction space in molecular systems

AL Dewyer, AJ Argüelles… - Wiley Interdisciplinary …, 2018 - Wiley Online Library
The area of reaction mechanism discovery simulation has taken considerable strides in
recent years. Novel methods that make hypotheses for elementary steps and …

Polarizable embedding QM/MM: the future gold standard for complex (bio) systems?

M Bondanza, M Nottoli, L Cupellini… - Physical Chemistry …, 2020 - pubs.rsc.org
Nowadays, hybrid QM/MM approaches are widely used to study (supra) molecular systems
embedded in complex biological matrices. However, in their common formulation, mutual …

Review on the QM/MM methodologies and their application to metalloproteins

CE Tzeliou, MA Mermigki, D Tzeli - Molecules, 2022 - mdpi.com
The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was
introduced in 1976, while the extensive acceptance of this methodology started in the 1990s …

Navigating the landscape of enzyme design: from molecular simulations to machine learning

J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …

Recent trends in quantum chemical modeling of enzymatic reactions

F Himo - Journal of the American Chemical Society, 2017 - ACS Publications
The quantum chemical cluster approach is a powerful method for investigating enzymatic
reactions. Over the past two decades, a large number of highly diverse systems have been …

Universal QM/MM approaches for general nanoscale applications

KS Csizi, M Reiher - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …