Finding multiple reaction pathways of ligand unbinding

Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways

(2018) Ariane Nunes-Alves et al.   BIOPHYSICAL JOURNAL

New approaches for computing ligand–receptor binding kinetics

(2018) Neil J Bruce et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conformational Sampling of a Biomolecular Rugged Energy Landscape

(2018) Jakub Rydzewski et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Frequency adaptive metadynamics for the calculation of rare-event kinetics

(2018) Yong Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

(2018) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways

(2018) J. Rydzewski et al.   Journal of Chemical Theory and Computation

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

(2018) Samuel D Lotz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unfolding Hidden Barriers by Active Enhanced Sampling

(2018) Jing Zhang et al.   PHYSICAL REVIEW LETTERS

Kinetics of Ligand–Protein Dissociation from All-Atom Simulations: Are We There Yet?

(2018) João Marcelo Lamim Ribeiro et al.   BIOCHEMISTRY

Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant

(2018) Victoria A. Feher et al.   BIOPHYSICAL JOURNAL

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways

(2017) Clark Templeton et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces

(2017) Elia Schneider et al.   PHYSICAL REVIEW LETTERS

Rare-event sampling in ligand diffusion

(2017) J. Rydzewski et al.   Physics of Life Reviews

Ligand diffusion in proteins via enhanced sampling in molecular dynamics

(2017) J. Rydzewski et al.   Physics of Life Reviews

Finding multiple reaction pathways via global optimization of action

(2017) Juyong Lee et al.   Nature Communications

Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations

(2017) J. Rydzewski et al.   Scientific Reports

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam

(2016) J. Rydzewski et al.   Journal of Chemical Theory and Computation

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

(2016) Yong Wang et al.   eLife

Memetic algorithms for ligand expulsion from protein cavities

(2015) J. Rydzewski et al.   JOURNAL OF CHEMICAL PHYSICS

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Beyond Microscopic Reversibility: Are Observable Nonequilibrium Processes Precisely Reversible?

(2011) Divesh Bhatt et al.   Journal of Chemical Theory and Computation

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward Quantitative Simulations of Carbon Monoxide Escape Pathways in Myoglobin†

(2008) Ron Elber et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Pathways of Maximum Likelihood for Rare Events in Nonequilibrium Systems: Application to Nucleation in the Presence of Shear

(2008) Matthias Heymann et al.   PHYSICAL REVIEW LETTERS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS