Peptide dimerization-dissociation rates from replica exchange molecular dynamics
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Peptide dimerization-dissociation rates from replica exchange molecular dynamics
Authors
Keywords
-
Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 147, Issue 15, Pages 152725
Publisher
AIP Publishing
Online
2017-10-12
DOI
10.1063/1.5004774
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Transition path sampling of rare events by shooting from the top
- (2017) Hendrik Jung et al. JOURNAL OF CHEMICAL PHYSICS
- Calculating transition rates from durations of transition paths
- (2017) Fangqiang Zhu JOURNAL OF CHEMICAL PHYSICS
- Kinetics from Replica Exchange Molecular Dynamics Simulations
- (2017) Lukas S. Stelzl et al. Journal of Chemical Theory and Computation
- Variational Identification of Markovian Transition States
- (2017) Linda Martini et al. Physical Review X
- On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics
- (2016) Tetsuro Nagai et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers’ Rate Theory
- (2016) Aaron T. Frank et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers
- (2016) Cathal T. Leahy et al. Journal of Physical Chemistry Letters
- Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins
- (2016) Martín Carballo-Pacheco et al. PROTEIN SCIENCE
- On performance measures for infinite swapping Monte Carlo methods
- (2015) J. D. Doll et al. JOURNAL OF CHEMICAL PHYSICS
- Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling
- (2015) Chao Lv et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Coupled folding and binding with 2D Window-Exchange Umbrella Sampling
- (2015) Alex Dickson et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
- (2015) Junchao Xia et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method
- (2014) Qing Lu et al. JOURNAL OF CHEMICAL PHYSICS
- Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
- (2014) Edina Rosta et al. Journal of Chemical Theory and Computation
- Note: Network random walk model of two-state protein folding: Test of the theory
- (2013) Alexander M. Berezhkovskii et al. JOURNAL OF CHEMICAL PHYSICS
- Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations
- (2012) Nicolae-Viorel Buchete BIOPHYSICAL JOURNAL
- Rare-event sampling: Occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods
- (2012) J. D. Doll et al. JOURNAL OF CHEMICAL PHYSICS
- Protein folding kinetics and thermodynamics from atomistic simulation
- (2012) S. Piana et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Are Peptides Good Two-State Folders?
- (2011) Alexander M. Berezhkovskii et al. Journal of Chemical Theory and Computation
- What Is the Time Scale for α-Helix Nucleation?
- (2011) David De Sancho et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations
- (2011) Edina Rosta et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- How Fast-Folding Proteins Fold
- (2011) K. Lindorff-Larsen et al. SCIENCE
- 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
- Error and efficiency of simulated tempering simulations
- (2010) Edina Rosta et al. JOURNAL OF CHEMICAL PHYSICS
- Exchange Often and Properly in Replica Exchange Molecular Dynamics
- (2010) Daniel J. Sindhikara et al. Journal of Chemical Theory and Computation
- Entropic barriers, transition states, funnels, and exponential protein folding kinetics: A simple model
- (2010) D. J. Bicout et al. PROTEIN SCIENCE
- Error and efficiency of replica exchange molecular dynamics simulations
- (2009) Edina Rosta et al. JOURNAL OF CHEMICAL PHYSICS
- Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics
- (2009) Weihua Zheng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
- (2008) Berk Hess et al. Journal of Chemical Theory and Computation
- Coarse Master Equations for Peptide Folding Dynamics†
- (2008) Nicolae-Viorel Buchete et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A temperature predictor for parallel tempering simulations
- (2008) Alexandra Patriksson et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Peptide folding kinetics from replica exchange molecular dynamics
- (2008) Nicolae-Viorel Buchete et al. PHYSICAL REVIEW E
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started