CHARMM at 45: Enhancements in accessibility, functionality, and speed

W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Hydrogen tunneling links protein dynamics to enzyme catalysis

JP Klinman, A Kohen - Annual review of biochemistry, 2013 - annualreviews.org
The relationship between protein dynamics and function is a subject of considerable
contemporary interest. Although protein motions are frequently observed during ligand …

Electron-volt neutron spectroscopy: beyond fundamental systems

C Andreani, M Krzystyniak, G Romanelli… - Advances in …, 2017 - Taylor & Francis
This work provides an up-to-date account of the use of electron-volt neutron spectroscopy in
materials research. This is a growing area of neutron science, capitalising upon the unique …

Connecting protein conformational dynamics with catalytic function as illustrated in dihydrofolate reductase

Y Fan, A Cembran, S Ma, J Gao - Biochemistry, 2013 - ACS Publications
Combined quantum mechanics/molecular mechanics molecular dynamics simulations
reveal that the M20 loop conformational dynamics of dihydrofolate reductase (DHFR) is …

Molecular modelling and simulations in cancer research

R Friedman, K Boye, K Flatmark - … et Biophysica Acta (BBA)-Reviews on …, 2013 - Elsevier
The complexity of cancer and the vast amount of experimental data available have made
computer-aided approaches necessary. Biomolecular modelling techniques are becoming …

Exploring the Role of Molecular Dynamics Simulations in Most Recent Cancer Research: Insights into Treatment Strategies

R Bozorgpour, S Sheybanikashani… - arXiv preprint arXiv …, 2023 - arxiv.org
Cancer is a complex disease that is characterized by uncontrolled growth and division of
cells. It involves a complex interplay between genetic and environmental factors that lead to …

Classical and Quantum Modeling of Li and Na Diffusion in FePO4

M Dixit, H Engel, R Eitan, D Aurbach… - The Journal of …, 2015 - ACS Publications
Lithium diffusion in olivine phosphates has been widely studied both experimentally and
theoretically. However, nuclear quantum effects (NQEs) of the Li ions have not been …

Nuclear quantum effects and kinetic isotope effects in enzyme reactions

A Vardi-Kilshtain, N Nitoker, DT Major - Archives of biochemistry and …, 2015 - Elsevier
Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly
specific chemical transformations. Studying the nature of rate enhancements and the …

Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase

AR Mhashal, Y Pshetitsky, CM Cheatum… - Journal of the …, 2018 - ACS Publications
In the present study, we address the effect of active site structure and dynamics of different
dihydrofolate reductase (DHFR) isoforms on the p K a of the bound substrate 7, 8 …

Collective reaction coordinate for hybrid quantum and molecular mechanics simulations: a case study of the hydride transfer in dihydrofolate reductase

D Doron, A Kohen, DT Major - Journal of Chemical Theory and …, 2012 - ACS Publications
The optimal description of the reaction coordinate in chemical systems is of great importance
in simulating condensed phase reactions. In the current work, we present a collective …