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

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

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

Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

(2016) Duncan E. Scott et al.   NATURE REVIEWS DRUG DISCOVERY

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

Estimation and uncertainty of reversible Markov models

(2015) Benjamin Trendelkamp-Schroer et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

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

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

Identification of slow molecular order parameters for Markov model construction

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

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

(2013) Frank Noé et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

(2013) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Atomistic Description of the Folding of a Dimeric Protein

(2013) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Free-energy landscape of protein oligomerization from atomistic simulations

(2013) A. Barducci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

Markov models of molecular kinetics: Generation and validation

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

Multistep Kinetics of the U1A–SL2 RNA Complex Dissociation

(2011) Divina Anunciado et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Adhesive water networks facilitate binding of protein interfaces

(2011) Mazen Ahmad et al.   Nature Communications

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

(2010) I. Buch et al.   Journal of Chemical Information and Modeling

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models

(2010) Gregory R. Bowman et al.   Journal of Chemical Theory and Computation

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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

Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches

(2008) Jakob Schluttig et al.   JOURNAL OF CHEMICAL PHYSICS