User profiles for Antonia S. J. S. Mey
Antonia SJS MeySenior Lecturer at the University of Edinburgh Verified email at ed.ac.uk Cited by 1733 |
Best practices for alchemical free energy calculations
Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …
associated with the transfer of molecules from one environment to another. The hallmark of …
Variational approach to molecular kinetics
…, G P�rez-Hern�ndez, ASJS Mey…�- Journal of chemical�…, 2014 - ACS Publications
The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator)
contain the essential information about the molecular thermodynamics and kinetics. This …
contain the essential information about the molecular thermodynamics and kinetics. This …
Assessment of binding affinity via alchemical free-energy calculations
M Kuhn, S Firth-Clark, P Tosco, ASJS Mey…�- Journal of Chemical�…, 2020 - ACS Publications
Free-energy calculations have seen increased usage in structure-based drug design. Despite
the rising interest, automation of the complex calculations and subsequent analysis of …
the rising interest, automation of the complex calculations and subsequent analysis of …
EMMA: a software package for Markov model building and analysis
…, B Trendelkamp-Schroer, ASJS Mey…�- Journal of chemical�…, 2012 - ACS Publications
The study of folding and conformational changes of macromolecules by molecular dynamics
simulations often requires the generation of large amounts of simulation data that are …
simulations often requires the generation of large amounts of simulation data that are …
[HTML][HTML] Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing
configuration-space-discretized simulation trajectories produced at different thermodynamic …
configuration-space-discretized simulation trajectories produced at different thermodynamic …
xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
Computing the equilibrium properties of complex systems, such as free energy differences, is
often hampered by rare events in the dynamics. Enhanced sampling methods may be used …
often hampered by rare events in the dynamics. Enhanced sampling methods may be used …
Dynamic properties of force fields
Molecular-dynamics simulations are increasingly used to study dynamic properties of
biological systems. With this development, the ability of force fields to successfully predict …
biological systems. With this development, the ability of force fields to successfully predict …
Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks
Free energy calculations are rapidly becoming indispensable in structure-enabled drug
discovery programs. As new methods, force fields, and implementations are developed, …
discovery programs. As new methods, force fields, and implementations are developed, …
Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins
ASJS Mey, PL Geissler, JP Garrahan�- Physical Review E, 2014 - APS
We explore the dynamical large deviations of a lattice heteropolymer model of a protein by
means of path sampling of trajectories. We uncover the existence of nonequilibrium …
means of path sampling of trajectories. We uncover the existence of nonequilibrium …
From proteins to ligands: decoding deep learning methods for binding affinity prediction
Accurate in silico prediction of protein–ligand binding affinity is important in the early stages
of drug discovery. Deep learning-based methods exist but have yet to overtake more …
of drug discovery. Deep learning-based methods exist but have yet to overtake more …