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

Kinetics from Replica Exchange Molecular Dynamics Simulations

(2017) Lukas S. Stelzl et al.   Journal of Chemical Theory and Computation

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding

(2017) Lane W. Votapka et al.   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

Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

(2017) Nuria Plattner et al.   Nature Chemistry

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

(2017) Pratyush Tiwary et al.   Science Advances

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

Recognition Dynamics of p53 and MDM2: Implications for Peptide Design

(2016) Karim M. ElSawy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein–Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide

(2016) Matthew C. Zwier et al.   Journal of Physical Chemistry Letters

Multiensemble Markov models of molecular thermodynamics and kinetics

(2016) Hao Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

(2015) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs

(2015) Maxwell I. Zimmerman et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer 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

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

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

(2015) Gregory R. Bowman 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

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations

(2014) S. Doerr et al.   Journal of Chemical Theory and Computation

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

(2014) Edina Rosta et al.   Journal of Chemical Theory and Computation

Efficient calculation of relative binding free energies by umbrella sampling perturbation

(2014) Fabian Zeller et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

(2014) Jordane Preto et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Conformational selection in protein binding and function

(2014) Thomas R. Weikl et al.   PROTEIN SCIENCE

Kinetic modulation of a disordered protein domain by phosphorylation

(2014) Nathaniel Stanley et al.   Nature Communications

Simulation tools for particle-based reaction-diffusion dynamics in continuous space

(2014) Johannes Schöneberg et al.   BMC Biophysics

Pharmacokinetics and the drug–target residence time concept

(2013) Göran Dahl 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

Multivalency as a Chemical Organization and Action Principle

(2012) Carlo Fasting et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Dynamics and mechanisms of coupled protein folding and binding reactions

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

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

(2012) G. R. Bowman 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

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

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

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

(2011) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The dynamics of drug-target interactions: drug-target residence time and its impact on efficacy and safety

(2010) Robert A Copeland   Expert Opinion on Drug Discovery

Systematic Mutational Analysis of Peptide Inhibition of the p53–MDM2/MDMX Interactions

(2010) Chong Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

(2010) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100

(2009) Shubhra Dastidar et al.   BMC BIOINFORMATICS

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Data-Based Inference of Generators for Markov Jump Processes Using Convex Optimization

(2009) Daan Crommelin et al.   MULTISCALE MODELING & SIMULATION

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX

(2009) M. Pazgier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Residence Time of Receptor−Ligand Complexes and Its Effect on Biological Function

(2008) Peter J. Tummino et al.   BIOCHEMISTRY

Coarse Master Equations for Peptide Folding Dynamics†

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

Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition

(2008) S. Shangary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA