Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration
We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …
simulations. We consider methods based on collective variable biasing and on tempering …
Understanding DNA under oxidative stress and sensitization: The role of molecular modeling
DNA is constantly exposed to damaging threats coming from oxidative stress, ie, from the
presence of free radicals and reactive oxygen species. Sensitization from exogenous and …
presence of free radicals and reactive oxygen species. Sensitization from exogenous and …
[HTML][HTML] Challenges in computational studies of enzyme structure, function and dynamics
ATP Carvalho, A Barrozo, D Doron, AV Kilshtain… - Journal of Molecular …, 2014 - Elsevier
In this review we give an overview of the field of Computational enzymology. We start by
describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel …
describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel …
Tautomer-specific deacylation and Ω-loop flexibility explain the carbapenem-hydrolyzing broad-spectrum activity of the KPC-2 β-lactamase
KPC-2 (Klebsiella pneumoniae carbapenemase-2) is a globally disseminated serine-β-
lactamase (SBL) responsible for extensive β-lactam antibiotic resistance in Gram-negative …
lactamase (SBL) responsible for extensive β-lactam antibiotic resistance in Gram-negative …
Adaptive finite temperature string method in collective variables
K Zinovjev, I Tunon - The Journal of Physical Chemistry A, 2017 - ACS Publications
Here we present a modified version of the on-the-fly string method for the localization of the
minimum free energy path in a space of arbitrary collective variables. In the proposed …
minimum free energy path in a space of arbitrary collective variables. In the proposed …
Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force
B Kim, R Snyder, M Nagaraju, Y Zhou… - Journal of chemical …, 2021 - ACS Publications
First-principles determination of free energy profiles for condensed-phase chemical
reactions is hampered by the daunting costs associated with configurational sampling on ab …
reactions is hampered by the daunting costs associated with configurational sampling on ab …
Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands
The determination of minimum free energy pathways (MFEP) is one of the most widely used
strategies to study reactive processes. For chemical reactions in complex environments, the …
strategies to study reactive processes. For chemical reactions in complex environments, the …
Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein
The transition of an α-helix to a β-sheet in proteins is among the most complex
conformational changes seen in biomolecular systems. Due to long time scales involved in …
conformational changes seen in biomolecular systems. Due to long time scales involved in …
Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
We combine molecular dynamics, statistical mechanics, and hybrid quantum
mechanics/molecular mechanics simulations to describe mechanistically the severe acute …
mechanics/molecular mechanics simulations to describe mechanistically the severe acute …
Reaction coordinates and transition states in enzymatic catalysis
K Zinovjev, I Tuñón - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Enzymatic reactions are complex chemical processes taking place in complex dynamic
environments. Theoretical characterization of these reactions requires the determination of …
environments. Theoretical characterization of these reactions requires the determination of …