Frequency adaptive metadynamics for the calculation of rare-event kinetics

New approaches for computing ligand–receptor binding kinetics

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

Characterizing Drug–Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches

(2017) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Determining energy barriers and selectivities of a multi-pathway system with infrequent metadynamics

(2017) Christopher D. Fu et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin–Streptavidin

(2017) Pratyush Tiwary   JOURNAL OF PHYSICAL CHEMISTRY B

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations

(2017) Rodrigo Casasnovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics

(2017) Yong Wang et al.   Chemical Science

Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations

(2017) Fabian Paul et al.   Nature Communications

How and when does an anticancer drug leave its binding site?

(2017) Pratyush Tiwary et al.   Science Advances

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

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

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations

(2016) Kelly L. Fleming et al.   JOURNAL OF PHYSICAL CHEMISTRY A

How a Kinase Inhibitor Withstands Gatekeeper Residue Mutations

(2016) Jagannath Mondal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient Estimation of Rare-Event Kinetics

(2016) Benjamin Trendelkamp-Schroer et al.   Physical Review X

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

(2016) Yong Wang et al.   eLife

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Variationally Optimized Free-Energy Flooding for Rate Calculation

(2015) James McCarty et al.   PHYSICAL REVIEW LETTERS

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

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

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

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

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dominant folding pathways of a WW domain

(2012) S. a Beccara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

(2011) David R. Glowacki et al.   Journal of Chemical Theory and Computation

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

(2011) Guillaume Bouvignies et al.   NATURE

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

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

(2010) Stefano Piana et al.   JOURNAL OF MOLECULAR BIOLOGY

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

The Trp-cage: optimizing the stability of a globular miniprotein

(2008) B. Barua et al.   PROTEIN ENGINEERING DESIGN & SELECTION