Identification of slow molecular order parameters for Markov model construction

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

Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide

(2012) Ganna Berezovska et al.   JOURNAL OF CHEMICAL PHYSICS

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Estimating the Eigenvalue Error of Markov State Models

(2012) Natasa Djurdjevac et al.   MULTISCALE MODELING & SIMULATION

Kinetic characterization of the critical step in HIV-1 protease maturation

(2012) S. K. Sadiq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

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

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

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

(2011) Xevi Biarnés et al.   COMPUTER PHYSICS COMMUNICATIONS

Intrinsically disordered proteins from A to Z

(2011) Vladimir N. Uversky   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

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

Relaxation mode analysis of a peptide system: Comparison with principal component analysis

(2011) Ayori Mitsutake et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

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

The Complex Folding Network of Single Calmodulin Molecules

(2011) J. Stigler et al.   SCIENCE

How Fast-Folding Proteins Fold

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

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein

(2011) Menahem Pirchi et al.   Nature Communications

The Free Energy Landscape of Small Molecule Unbinding

(2011) Danzhi Huang et al.   PLoS Computational Biology

Dynamics of protein folding: Probing the kinetic network of folding–unfolding transitions with experiment and theory

(2010) Ginka S. Buchner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

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

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

Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

(2010) Michele Seeber et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family

(2010) Beth G. Wensley et al.   NATURE

Full distance-resolved folding energy landscape of one single protein molecule

(2010) J. C. M. Gebhardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

(2010) Isabella Daidone et al.   PLoS Computational Biology

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

Transition Path Theory for Markov Jump Processes

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

Nucleosome disassembly intermediates characterized by single-molecule FRET

(2009) A. Gansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational transitions in DNA polymerase I revealed by single-molecule FRET

(2009) Y. Santoso 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

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS

Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation

(2008) Frank Noé et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse Master Equations for Peptide Folding Dynamics†

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