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© Research
Publication : Biophysical journal

Linking well-tempered metadynamics simulations with experiments

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Biophysical journal - 19 May 2010

Barducci A, Bonomi M, Parrinello M

Link to Pubmed [PMID] – 20441734

Biophys. J. 2010 May;98(9):L44-6

Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data.