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The quantum chemical cluster approach in biocatalysis
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 …
active sites and reaction mechanisms for more than two decades. In this methodology, a …
Computational modeling of realistic cell membranes
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 …
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
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 …
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 …
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 …
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
Simulation studies of amyloidogenic polypeptides and their aggregates
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 …
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 …
Chemical surfactants are omnipresent in consumer products, but they are the subject of
environmental concerns. For this reason, the complete replacement of petrochemical …
environmental concerns. For this reason, the complete replacement of petrochemical …
Biology and medicine in the landscape of quantum advantages
Quantum computing holds substantial potential for applications in biology and medicine,
spanning from the simulation of biomolecules to machine learning methods for subty** …
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 …
quality commodity hardware that can offer new ways to teach, communicate, and engage …
Protein storytelling through physics
BACKGROUND Understanding biology, particularly at the level of actionable drug
discovery, is often a matter of develo** accurate stories about how proteins work. This …
discovery, is often a matter of develo** accurate stories about how proteins work. This …