A molecular simulation protocol to avoid sampling redundancy and discover new states

For biomacromolecules or their assemblies, experimental knowledge is often restricted to specific states. Ambiguity pervades simulations of these complex systems because there is no prior knowledge of relevant phase space domains, and sampling recurrence is difficult to achieve. In molecular dynamic...

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Bibliographic Details
Published in:	Biochimica et biophysica acta Vol. 1850; no. 5; pp. 889 - 902
Main Authors:	Bacci, Marco, Vitalis, Andreas, Caflisch, Amedeo
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01.05.2015
Subjects:	Algorithms Biomolecules Enhanced sampling Gibbs free energy Kinetics Molecular dynamics Molecular Dynamics Simulation peptides Protein Stability Protein Structure, Secondary Proteins - chemistry Proteins - metabolism Reproducibility of Results Scalable algorithm Simulation convergence Structure-Activity Relationship Thermodynamics Transition path PIGS REX MSM Transition path Simulation convergence Molecular dynamics RMSD Enhanced sampling PCA CS Scalable algorithm MC MD Biomolecules CLD PES
ISSN:	0304-4165, 0006-3002, 1872-8006
Online Access:	Get full text
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