Quantitative comparison of adaptive sampling methods for protein dynamics

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

(2018) João Marcelo Lamim Ribeiro et al.   JOURNAL OF CHEMICAL PHYSICS

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

(2018) Christoph Wehmeyer et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics Enhanced Markov Modeling of Protein Dynamics

(2018) Mithun Biswas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Girsanov reweighting for metadynamics simulations

(2018) Luca Donati et al.   JOURNAL OF CHEMICAL PHYSICS

Author Correction: VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

(2017) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Girsanov reweighting for path ensembles and Markov state models

(2017) L. Donati et al.   JOURNAL OF CHEMICAL PHYSICS

Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias

(2017) Feliks Nüske et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2017) Nuria Plattner et al.   Nature Chemistry

Adaptive simulations, towards interactive protein-ligand modeling

(2017) Daniel Lecina et al.   Scientific Reports

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information

(2017) Zahra Shamsi et al.   Scientific Reports

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling

(2016) Frank Noé et al.   Journal of Chemical Theory and Computation

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

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

MHC class II complexes sample intermediate states along the peptide exchange pathway

(2016) Marek Wieczorek et al.   Nature Communications

Efficient Estimation of Rare-Event Kinetics

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

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps

(2015) Lorenzo Boninsegna 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

WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis

(2015) Matthew C. Zwier 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

A Data–Driven Approximation of the Koopman Operator: Extending Dynamic Mode Decomposition

(2015) Matthew O. Williams et al.   JOURNAL OF NONLINEAR SCIENCE

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

WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm

(2014) Alex Dickson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

Identification of slow molecular order parameters for Markov model construction

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

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

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

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

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

Determination of reaction coordinates via locally scaled diffusion map

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

Markov models of molecular kinetics: Generation and validation

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

Characterization and Rapid Sampling of Protein Folding Markov State Model Topologies

(2011) Jeffrey K. Weber et al.   Journal of Chemical Theory and Computation

Delineation of Folding Pathways of a β-Sheet Miniprotein

(2011) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Fast-Folding Proteins Fold

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

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

Coarse Master Equations for Peptide Folding Dynamics†

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

Diffusive reaction dynamics on invariant free energy profiles

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

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS