Computational design of enzymes for biotechnological applications
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their
natural effectiveness has been fine-tuned as a result of millions of years of natural evolution …
natural effectiveness has been fine-tuned as a result of millions of years of natural evolution …
Transition states, analogues, and drug development
VL Schramm - ACS chemical biology, 2013 - ACS Publications
Enzymes achieve their transition states by dynamic conformational searches on the
femtosecond to picosecond time scale. Mimics of reactants at enzymatic transition states …
femtosecond to picosecond time scale. Mimics of reactants at enzymatic transition states …
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 …
Current advances in design and engineering strategies of industrial enzymes
T Dinmukhamed, Z Huang, Y Liu, X Lv, J Li… - Systems Microbiology …, 2021 - Springer
Enzymes are considered as functional proteins, also known as biocatalysts, which are
required for normal cellular function. The commercial production of enzymes with distinct …
required for normal cellular function. The commercial production of enzymes with distinct …
Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here?
Adaptive quantum‐mechanics/molecular‐mechanics (QM/MM) methods feature on‐the‐fly
reclassification of atoms as QM or MM during a molecular dynamics (MD) simulation …
reclassification of atoms as QM or MM during a molecular dynamics (MD) simulation …
Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase
RPP Neves, PA Fernandes… - Proceedings of the …, 2017 - National Acad Sciences
We explore the enzymatic mechanism of the reduction of glutathione disulfide (GSSG) by the
reduced a domain of human protein disulfide isomerase (hPDI) with atomistic resolution. We …
reduced a domain of human protein disulfide isomerase (hPDI) with atomistic resolution. We …
Recent developments in QM/MM methods towards open-boundary multi-scale simulations
S Pezeshki, H Lin - Molecular Simulation, 2015 - Taylor & Francis
Combined quantum mechanics/molecular mechanics (QM/MM) methods have been widely
used in multi-scale modelling and simulations of physical, chemical and biological …
used in multi-scale modelling and simulations of physical, chemical and biological …
The increasing role of QM/MM in drug discovery
Since its first appearance in 1976, the quantum mechanics/molecular mechanics (QM/MM)
approach has mostly been used to study the chemical reactions of enzymes, which are …
approach has mostly been used to study the chemical reactions of enzymes, which are …
Nanoplasmonic sensor optimization via digital imaging analysis and antibody evolution
J Liang, Y Qin, Y Yang, Z Song, Y Li, GL Liu… - Sensors and Actuators B …, 2024 - Elsevier
Localized surface plasmon resonance (LSPR) biosensors have emerged as powerful
analytical tools for detecting biomolecules like proteins, DNA, and RNA across biomedical …
analytical tools for detecting biomolecules like proteins, DNA, and RNA across biomedical …
Adaptive partitioning QM/MM for molecular dynamics simulations: 6. Proton transport through a biological channel
Adaptive quantum-mechanics/molecular-mechanics (QM/MM) dynamics simulations feature
on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories …
on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories …