Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

Estimation of Relaxation Modulus of Polymer Melts by Molecular Dynamics Simulations: Application of Relaxation Mode Analysis

(2015) Nobuyuki Iwaoka et al.   JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Perspective: Markov models for long-timescale biomolecular dynamics

(2014) C. R. Schwantes et al.   JOURNAL OF CHEMICAL PHYSICS

Heterogeneous Chain Dynamics in a Supercooled Polymer Melt: Relaxation Mode Analysis Study

(2014) Nobuyuki Iwaoka et al.   JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN

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

Relaxation of a Single Dendrimer

(2013) Nobuyuki Iwaoka et al.   JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN

Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics method

(2013) Hisashi Okumura   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

(2012) Petra Kührová et al.   BIOPHYSICAL JOURNAL

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL 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

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

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

Exploring the Folding Free Energy Landscape of a β-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method

(2011) Ryuhei Harada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

Transition networks for modeling the kinetics of conformational change in macromolecules

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

Coarse Master Equations for Peptide Folding Dynamics†

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

Relaxation of a Single Knotted Ring Polymer

(2008) Shinya Saka et al.   JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN