Network models for molecular kinetics and their initial applications to human health

Intrinsic disorder in proteins associated with neurodegenerative diseases

(2010) Vladimir et al.   Frontiers in Bioscience-Landmark

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

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

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

(2009) Vincent Voelz et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

(2009) Sergio Bacallado et al.   JOURNAL OF CHEMICAL PHYSICS

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

Topological methods for exploring low-density states in biomolecular folding pathways

(2009) Yuan Yao et al.   JOURNAL OF CHEMICAL PHYSICS

The Predicted Structure of the Headpiece of the Huntingtin Protein and Its Implications on Huntingtin Aggregation

(2009) Nicholas W. Kelley et al.   JOURNAL OF MOLECULAR BIOLOGY

ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations

(2009) S. Muff et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

The Roles of Entropy and Kinetics in Structure Prediction

(2009) Gregory R. Bowman et al.   PLoS One

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

(2009) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic gating of the proton pump in cytochrome c oxidase

(2009) Y. C. Kim 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

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

(2009) D. Wang et al.   SCIENCE

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Transition networks for modeling the kinetics of conformational change in macromolecules

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

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

(2008) Vincent B Chu 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

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach

(2008) Nicholas W. Kelley et al.   JOURNAL OF CHEMICAL PHYSICS

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

(2008) Xuhui Huang et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

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

Structural Insight into RNA Hairpin Folding Intermediates

(2008) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simulated tempering yields insight into the low-resolution Rosetta scoring functions

(2008) Gregory R. Bowman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

(2008) Sichun Yang et al.   PLoS Computational Biology

Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg

(2007) Alessandra Villa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin

(2007) Angel E. Garcia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY