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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Vydané v:	Biochimica et biophysica acta Ročník 1850; číslo 5; s. 889 - 902
Hlavní autori:	Bacci, Marco, Vitalis, Andreas, Caflisch, Amedeo
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Netherlands Elsevier B.V 01.05.2015
Predmet:	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
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