Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation
Young Min Rhee,Vijay S. Pande +1 more
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TL;DR: An algorithm to calculate a canonical distribution from molecular dynamics simulation of protein folding based on the replica exchange method, which results in the first example of a replica exchange algorithm that samples a folded structure starting from a completely unfolded state.
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About: This article is published in Biophysical Journal. The article was published on 01 Feb 2003. and is currently open access. The article focuses on the topics: Folding (DSP implementation) & Replica.
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Citations
The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Heng Li,Jue Ruan,Richard Durbin +2 more
TL;DR: This work describes the software MAQ, software that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample.
Replica Exchange with Solute Scaling: A more efficient version of Replica Exchange with Solute Tempering (REST2)
TL;DR: A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for the sampling of aqueous protein solutions in which there are large-scale solute conformation changes.
Enhanced sampling techniques in molecular dynamics simulations of biological systems
TL;DR: An overview over theses sampling methods is presented in an attempt to shed light on which should be selected depending on the type of system property studied, and whether metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics.
701
Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations
Eric J. Sorin,Vijay S. Pande +1 more
TL;DR: The ensemble folding of two 21-residue alpha-helical peptides has been studied using all-atom simulations under several variants of the AMBER potential in explicit solvent and extensive sampling results in complete convergence to ensemble equilibrium.
697
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