Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece

2007/10/02 by Daniel L. Ensign, Peter M. Kasson, Vijay S. Pande · 10 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Materials Science · #Actin #Chemical physics #Chemistry #Computational chemistry #Computer science #Contact order #Crystallography #Downhill folding #Enzyme Structure and Function #Folding (DSP implementation) #Folding funnel #Markov chain #Molecular dynamics #Native state #Phi value analysis #Photosynthetic Processes and Mechanisms #Physics #Protein Structure and Dynamics #Protein folding #Quenching (fluorescence) #Relaxation (psychology) #Villin

paper · doi:10.1016/j.jmb.2007.09.069

openalex publication_date 2007/10/02 · crossref created 2007/10/02 · crossref issued 2007/11/01 · crossref published 2007/11/01 · crossref published-print 2007/11/01 · crossref deposited 2019/01/03 · openalex created_date 2025/10/10 · crossref indexed 2026/01/13 · openalex updated_date 2026/08/01

Citations

• Constant pressure molecular dynamics for molecular systems
• GROMACS: A message-passing parallel molecular dynamics implementation
• Canonical dynamics: Equilibrium phase-space distributions
• A molecular dynamics method for simulations in the canonical ensemble
• Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing
• Polymorphic transitions in single crystals: A new molecular dynamics method
• How Well Can Simulation Predict Protein Folding Kinetics and Thermodynamics?
• Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
• GROMACS 3.0: a package for molecular simulation and trajectory analysis

Cited by

• Accelerating molecular dynamic simulation on graphics processing units
• Protein folded states are kinetic hubs
• Atomistic molecular simulations of protein folding
• Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories
• Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments
• Taming the complexity of protein folding
• Studying functional dynamics in bio-molecules using accelerated molecular dynamics
• Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
• Millisecond-scale molecular dynamics simulations on Anton
• Folding@home [wikipedia]