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

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Variational tensor approach for approximating the rare-event kinetics of macromolecular systems

(2016) Feliks Nüske et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Gaussian Markov transition models of molecular kinetics

(2015) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Variational cross-validation of slow dynamical modes in molecular kinetics

(2015) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Estimation and uncertainty of reversible Markov models

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

A Basis Set for Peptides for the Variational Approach to Conformational Kinetics

(2015) F. Vitalini et al.   Journal of Chemical Theory and Computation

Modeling Molecular Kinetics with tICA and the Kernel Trick

(2015) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

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

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

Crystal structure of the dynamin tetramer

(2015) Thomas F. Reubold et al.   NATURE

PNAS Plus Significance Statements

(2015)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudogenerators of Spatial Transfer Operators

(2015) Andreas Bittracher et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske 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

Flows in Complex Networks: Theory, Algorithms, and Application to Lennard–Jones Cluster Rearrangement

(2014) Maria Cameron et al.   JOURNAL OF STATISTICAL PHYSICS

Optimal Estimation of Free Energies and Stationary Densities from Multiple Biased Simulations

(2014) Hao Wu et al.   MULTISCALE MODELING & SIMULATION

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

(2014) D.-A. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

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

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

A structure-preserving numerical discretization of reversible diffusions

(2013) Carsten Hartmann et al.   Communications in Mathematical Sciences

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

(2013) Benjamin Lindner et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution

(2013) Benjamin Trendelkamp-Schroer et al.   JOURNAL OF 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

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

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

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

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

In This Issue

(2012)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics

(2011) Bettina G. Keller et al.   CHEMICAL PHYSICS

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

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

Markov state models based on milestoning

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

Markov models of molecular kinetics: Generation and validation

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

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments

(2011) John D. Chodera et al.   PHYSICAL REVIEW LETTERS

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

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

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

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

Dynamic mode decomposition of numerical and experimental data

(2010) PETER J. SCHMID   JOURNAL OF FLUID MECHANICS

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

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

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

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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

Spectral analysis of nonlinear flows

(2009) CLARENCE W. ROWLEY et al.   JOURNAL OF FLUID MECHANICS

Transition Path Theory for Markov Jump Processes

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

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

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