How wet should be the reaction coordinate for ligand unbinding?

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

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

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics

(2016) Pratyush Tiwary et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

(2016) Ivan Teo et al.   Journal of Chemical Theory and Computation

Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding

(2016) R. Gregor Weiß et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes

(2015) Purushottam D. Dixit et al.   Journal of Chemical Theory and Computation

The drug–target residence time model: a 10-year retrospective

(2015) Robert A. Copeland   NATURE REVIEWS DRUG DISCOVERY

Role of water and steric constraints in the kinetics of cavity–ligand unbinding

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

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

Locating landmarks on high-dimensional free energy surfaces

(2015) Ming Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase

(2014) Jagannath Mondal et al.   Journal of Chemical Theory and Computation

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

(2014) Matteo Salvalaglio et al.   Journal of Chemical Theory and Computation

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

(2014) Gerhard Hummer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Recognition and Ligand Association

(2013) Riccardo Baron et al.   Annual Review of Physical Chemistry

PLUMED 2: New feathers for an old bird

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

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Solvent fluctuations in hydrophobic cavity–ligand binding kinetics

(2013) Piotr Setny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How hydrophobic drying forces impact the kinetics of molecular recognition

(2013) J. Mondal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of maximum entropy and maximum caliber in statistical physics

(2013) Steve Pressé et al.   REVIEWS OF MODERN PHYSICS

Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse?

(2012) Jingyuan Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Voltage Gating in Potassium Channels

(2012) M. O. Jensen et al.   SCIENCE

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes

(2011) Joseph A. Morrone et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simplifying the representation of complex free-energy landscapes using sketch-map

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluctuations of Water near Extended Hydrophobic and Hydrophilic Surfaces

(2010) Amish J. Patel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION