289 citations · 549 across the 10 of their papers we have counts for
11 papers
LiveCoMS Roundtable: Discussing Markov state models after two decades of development v1.0
Daniel M. Zuckerman, Gregory R. Bowman, Amedeo Caflisch +14
Markov state models (MSMs) play a central role in the analysis of molecular dynamics (MD) simulations for biomolecules, and MSM methodologies have been under continual development…
Protein Dynamics Beyond Structure Prediction
Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo +41
The ability to predict protein three-dimensional structures from amino acid sequences is a landmark achievement in molecular biology, where recent deep learning approaches such as…
Dirac--Bianconi Graph Neural Networks -- Enabling Non-Diffusive Long-Range Graph Predictions
Christian Nauck, Rohan Gorantla, Michael Lindner +3
The geometry of a graph is encoded in dynamical processes on the graph. Many graph neural network (GNN) architectures are inspired by such dynamical systems, typically based on the…
SILVR: Guided Diffusion for Molecule Generation
Nicholas T. Runcie, Antonia S. J. S. Mey
Computationally generating novel synthetically accessible compounds with high affinity and low toxicity is a great challenge in drug design. Machine-learning models beyond conventi…
What geometrically constrained folding models can tell us about real-world protein contact maps
Nora Molkenthin, J. J. Güven, Steffen Mühle +1
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models,…
Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks
David F. Hahn, Christopher I. Bayly, Hannah E. Bruce Macdonald +8
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing…
Best Practices for Alchemical Free Energy Calculations
Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald +11
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…
Geometric constraints in protein folding
Nora Molkenthin, Steffen Mühle, Antonia S J S Mey +1
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids.…
Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
Hao Wu, Antonia S. J. S. Mey, Edina Rosta +1
We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic…
xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
Antonia S. J. S. Mey, Hao Wu, Frank Noé
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 in…
Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins
Antonia S. J. S. Mey, Phillip L. Geissler, Juan P. Garrahan
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 non-equilibrium dynam…