Equilibration and sampling in molecular dynamics simulations of biomolecules (original) (raw)
Related papers
Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins
Cecilia Clementi, Amarda Shehu
Algorithmica, 2007
Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance
Biophysical Journal, 2004
Molecular Fluctuations as a Ruler of Force-Induced Protein Conformations
Nano Letters, 2021
Simulated dynamics and biological macromolecules
Reports on Progress in Physics, 2003
Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins
Raffaello Potestio, Vincenzo Carnevale
Multiscale Approaches to Protein Modeling, 2010
2017
Rapid determination of RMSDs corresponding to macromolecular rigid body motions
Journal of Computational Chemistry, 2014
Molecular mechanics in biology: from structure to function, taking account of solvation
Annual review of biophysics and biomolecular structure, 1994
Journal of Molecular Biology, 1995
The Journal of Chemical Physics, 2013
Biochemistry, 1997
ChemPhysChem, 2020
Local Fluctuations and Conformational Transitions in Proteins
Journal of Chemical Theory and Computation, 2012
MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
2011
A Physical Picture of Protein Dynamics and Conformational Changes
Journal of Biological Physics, 2007
Long-time mean-square displacements in proteins
Physical Review E, 2013
Proteins: Structure, Function, and Bioinformatics, 2011
Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution
FEBS Letters, 2000
Molecular Dynamics and the Accuracy of Numerically Computed Averages
The Journal of Physical Chemistry B, 2020
Complexity at the Molecular Level : A Dynamic View of Biomolecules Obtained by NMR
1999
Continuum models for low-frequency dynamics of macromolecules and vesicles /
Relaxation time prediction for a light switchable peptide by molecular dynamics
Physical Chemistry Chemical Physics, 2010
Free energy determination of polypeptide conformations generated by molecular dynamics
Macromolecules, 1984
An Efficient Null Model for Conformational Fluctuations in Proteins
Jesper Ferkinghoff-borg, Simon Olsson, Wouter Boomsma
Structure, 2012
Book review: Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
1990
Proceedings of the National Academy of Sciences, 2005
Molecular dynamics of conformational substates for a simplified protein model
The Journal of Chemical Physics, 1994
The consistency of large concerted motions in proteins in molecular dynamics simulations
Biophysical Journal, 1996
Unit‐vector RMS (URMS) as a tool to analyze molecular dynamics trajectories
Proteins-structure Function and Bioinformatics, 1999
Journal of Physics: Condensed Matter, 2005
Biochemistry, 2004
Proteins: Structure, Function, and Bioinformatics, 2006
Diffusion of a protein in configuration space
1995