Catch bond-like kinetics of helix cracking: Network analysis by molecular dynamics and Milestoning

Force-Clamp Analysis Techniques Give Highest Rank to Stretched Exponential Unfolding Kinetics in Ubiquitin

(2012) Herbert Lannon et al.   BIOPHYSICAL JOURNAL

Multiple barriers in forced rupture of protein complexes

(2012) Changbong Hyeon et al.   JOURNAL OF CHEMICAL PHYSICS

Early Events in Helix Unfolding under External Forces: A Milestoning Analysis

(2012) Steven M. Kreuzer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unassisted Transport of N-Acetyl-l-tryptophanamide through Membrane: Experiment and Simulation of Kinetics

(2012) Alfredo E. Cardenas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Experiments and Comprehensive Simulations of the Formation of a Helical Turn

(2012) Gouri S. Jas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein

(2012) B. Jagannathan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Revisiting and Computing Reaction Coordinates with Directional Milestoning

(2011) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY A

What Is the Time Scale for α-Helix Nucleation?

(2011) David De Sancho et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Locating the Barrier for Folding of Single Molecules under an External Force

(2011) Olga K. Dudko et al.   PHYSICAL REVIEW LETTERS

Fast-folding  -helices as reversible strain absorbers in the muscle protein myomesin

(2011) F. Berkemeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Milestoning without a Reaction Coordinate

(2010) Peter Májek et al.   Journal of Chemical Theory and Computation

Maximum Flux Transition Paths of Conformational Change

(2010) Ruijun Zhao et al.   Journal of Chemical Theory and Computation

Helix Formation in a Pentapeptide: Experiment and Force-field Dependent Dynamics

(2010) Wendy A. Hegefeld et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

(2009) Alexander Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetics of Helix Unfolding: Molecular Dynamics Simulations with Milestoning†

(2009) Krzysztof Kuczera et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catch-Bond Mechanism of Force-Enhanced Adhesion: Counterintuitive, Elusive, but … Widespread?

(2008) Evgeni V. Sokurenko et al.   Cell Host & Microbe

FimH Forms Catch Bonds That Are Enhanced by Mechanical Force Due to Allosteric Regulation

(2008) Olga Yakovenko et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide folding kinetics from replica exchange molecular dynamics

(2008) Nicolae-Viorel Buchete et al.   PHYSICAL REVIEW E

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation