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 …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Development and benchmarking of open force field v1. 0.0—the parsley small-molecule force field

Y Qiu, DGA Smith, S Boothroyd, H Jang… - Journal of chemical …, 2021 - ACS Publications
We present a methodology for defining and optimizing a general force field for classical
molecular simulations, and we describe its use to derive the Open Force Field 1.0. 0 small …

Biomolecular modeling thrives in the age of technology

T Schlick, S Portillo-Ledesma - Nature computational science, 2021 - nature.com
The biomolecular modeling field has flourished since its early days in the 1970s due to the
rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase …

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 …

Simulation studies of amyloidogenic polypeptides and their aggregates

IM Ilie, A Caflisch - Chemical reviews, 2019 - ACS Publications
Amyloids, fibrillar assembly of (poly) peptide chains, are associated with neurodegenerative
illnesses such as Alzheimer's and Parkinson's diseases, for which there are no cures. The …

Self-assembly, interfacial properties, interactions with macromolecules and molecular modelling and simulation of microbial bio-based amphiphiles (biosurfactants). A …

N Baccile, C Seyrig, A Poirier, S Alonso-de Castro… - Green …, 2021 - pubs.rsc.org
Chemical surfactants are omnipresent in consumer products, but they are the subject of
environmental concerns. For this reason, the complete replacement of petrochemical …

Biology and medicine in the landscape of quantum advantages

BA Cordier, NPD Sawaya… - Journal of the …, 2022 - royalsocietypublishing.org
Quantum computing holds substantial potential for applications in biology and medicine,
spanning from the simulation of biomolecules to machine learning methods for subty** …

Teaching enzyme catalysis using interactive molecular dynamics in virtual reality

SJ Bennie, KE Ranaghan, H Deeks… - Journal of Chemical …, 2019 - ACS Publications
The reemergence of virtual reality (VR) in the past few years has led to affordable, high-
quality commodity hardware that can offer new ways to teach, communicate, and engage …

Protein storytelling through physics

E Brini, C Simmerling, K Dill - Science, 2020 - science.org
BACKGROUND Understanding biology, particularly at the level of actionable drug
discovery, is often a matter of develo** accurate stories about how proteins work. This …