scholarly journals Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

2013 ◽  
Vol 138 (9) ◽  
pp. 094112 ◽  
Author(s):  
Andrea Cavalli ◽  
Carlo Camilloni ◽  
Michele Vendruscolo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Maximum Entropy ◽  
Maximum Entropy Principle ◽  
Structural Ensembles ◽  
Entropy Principle ◽  
Structural Restraints ◽  
Dynamics Simulations

Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields

2018 ◽  
Vol 20 (13) ◽  
pp. 8676-8684 ◽  
Author(s):  
Yanhua Ouyang ◽  
Likun Zhao ◽  
Zhuqing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Structural Ensembles ◽  
Dynamics Simulations

The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.

scholarly journals Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins

Structure ◽  
2010 ◽  
Vol 18 (8) ◽  
pp. 923-933 ◽  
Author(s):  
Paul Robustelli ◽  
Kai Kohlhoff ◽  
Andrea Cavalli ◽  
Michele Vendruscolo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts ◽  
Structural Restraints ◽  
Dynamics Simulations

scholarly journals Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

2017 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Scott D. Kennedy ◽  
Douglas H. Turner ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Overhauser Effect ◽  
Conformational Dynamics ◽  
Maximum Entropy Principle ◽  
Coupling Constants ◽  
Scalar Coupling ◽  
Conformational Ensemble ◽  
Entropy Principle ◽  
Nuclear Overhauser ◽  
Dynamics Simulations

We determine the conformational ensemble of four RNA tetranucleotides by using available nuclear magnetic spectroscopy data in conjunction with extensive atomistic molecular dynamics simulations. This combination is achieved by applying a reweighting scheme based on the maximum entropy principle. We provide a quantitative estimate for the population of different conformational states by considering different NMR parameters, including distances derived from nuclear Overhauser effect intensities and scalar coupling constants. We show the usefulness of the method as a general tool for studying the conformational dynamics of flexible biomolecules as well as for detecting inaccuracies in molecular dynamics force fields.

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