skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on September 24, 2021

Title: A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems

Authors:
ORCiD logo [1]; ORCiD logo [1];  [2]
  1. Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, USA
  2. Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, USA, Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1664623
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Name: Journal of Chemical Physics Journal Volume: 153 Journal Issue: 12; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics
Country of Publication:
United States
Language:
English

Citation Formats

Ovchinnikov, Victor, Conti, Simone, and Karplus, Martin. A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems. United States: N. p., 2020. Web. https://doi.org/10.1063/5.0018026.
Ovchinnikov, Victor, Conti, Simone, & Karplus, Martin. A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems. United States. https://doi.org/10.1063/5.0018026
Ovchinnikov, Victor, Conti, Simone, and Karplus, Martin. Mon . "A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems". United States. https://doi.org/10.1063/5.0018026.
@article{osti_1664623,
title = {A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems},
author = {Ovchinnikov, Victor and Conti, Simone and Karplus, Martin},
abstractNote = {},
doi = {10.1063/5.0018026},
journal = {Journal of Chemical Physics},
number = 12,
volume = 153,
place = {United States},
year = {2020},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on September 24, 2021
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Enhanced sampling and applications in protein folding in explicit solvent
journal, June 2010

  • Zhang, Cheng; Ma, Jianpeng
  • The Journal of Chemical Physics, Vol. 132, Issue 24
  • DOI: 10.1063/1.3435332

Accelerating molecular dynamic simulation on graphics processing units
journal, April 2009

  • Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal
  • Journal of Computational Chemistry, Vol. 30, Issue 6
  • DOI: 10.1002/jcc.21209

Parallel continuous simulated tempering and its applications in large-scale molecular simulations
journal, July 2014

  • Zang, Tianwu; Yu, Linglin; Zhang, Chong
  • The Journal of Chemical Physics, Vol. 141, Issue 4
  • DOI: 10.1063/1.4890038

Conformational sampling for the impatient
journal, February 2004


Functionality maps of binding sites: A multiple copy simultaneous search method
journal, September 1991

  • Miranker, Andrew; Karplus, Martin
  • Proteins: Structure, Function, and Genetics, Vol. 11, Issue 1
  • DOI: 10.1002/prot.340110104

New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres
journal, October 1984

  • Frenkel, Daan; Ladd, Anthony J. C.
  • The Journal of Chemical Physics, Vol. 81, Issue 7
  • DOI: 10.1063/1.448024

A Minimal Peptide Scaffold for β-Turn Display:  Optimizing a Strand Position in Disulfide-Cyclized β-Hairpins
journal, January 2001

  • Cochran, Andrea G.; Tong, Ricky T.; Starovasnik, Melissa A.
  • Journal of the American Chemical Society, Vol. 123, Issue 4
  • DOI: 10.1021/ja003369x

Replica-exchange molecular dynamics method for protein folding
journal, November 1999


Energy equipartitioning in the classical time‐dependent Hartree approximation
journal, May 1991

  • Straub, John E.; Karplus, Martin
  • The Journal of Chemical Physics, Vol. 94, Issue 10
  • DOI: 10.1063/1.460250

CHARMM: The biomolecular simulation program
journal, July 2009

  • Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
  • Journal of Computational Chemistry, Vol. 30, Issue 10
  • DOI: 10.1002/jcc.21287

Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
journal, December 1990

  • Elber, R.; Karplus, M.
  • Journal of the American Chemical Society, Vol. 112, Issue 25
  • DOI: 10.1021/ja00181a020

Pi Release from Myosin: A Simulation Analysis of Possible Pathways
journal, March 2010


Drug Design by Generalized-Ensemble Simulations
journal, June 2011


Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

A random number generator based on the combination of four LCGs
journal, May 1997


Multidimensional replica-exchange method for free-energy calculations
journal, October 2000

  • Sugita, Yuji; Kitao, Akio; Okamoto, Yuko
  • The Journal of Chemical Physics, Vol. 113, Issue 15
  • DOI: 10.1063/1.1308516

Modified Replica Exchange Simulation Methods for Local Structure Refinement
journal, April 2005

  • Cheng, Xiaolin; Cui, Guanglei; Hornak, Viktor
  • The Journal of Physical Chemistry B, Vol. 109, Issue 16
  • DOI: 10.1021/jp045437y

Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model: Refining Protein Structures
journal, September 2018

  • Ma, Tianqi; Zang, Tianwu; Wang, Qinghua
  • Protein Science, Vol. 27, Issue 10
  • DOI: 10.1002/pro.3486

String method in collective variables: Minimum free energy paths and isocommittor surfaces
journal, July 2006

  • Maragliano, Luca; Fischer, Alexander; Vanden-Eijnden, Eric
  • The Journal of Chemical Physics, Vol. 125, Issue 2
  • DOI: 10.1063/1.2212942

Stochastic boundary conditions for molecular dynamics simulations of ST2 water
journal, March 1984


The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
journal, June 2009

  • Schubert, Christian R.; Stultz, Collin M.
  • Journal of Computer-Aided Molecular Design, Vol. 23, Issue 8
  • DOI: 10.1007/s10822-009-9287-y