Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.
|Title||Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.|
|Publication Type||Journal Article|
|Year of Publication||2010|
|Authors||Emperador, Agustí, Meyer Tim, and Orozco Modesto|
|Date Published||2010 Jan|
|Keywords||Computer Simulation, Databases, Molecular Dynamics Simulation, Principal Component Analysis, Protein, Protein Conformation, Proteins|
We have applied all atoms discrete molecular dynamics (DMD) based on a quasi-physical potential to study the flexibility of an extended set of proteins for which atomistic MD simulations are available. The method uses pure physical potentials supplemented by information on secondary structure and despite its simplicity is able to reproduce with good accuracy the dynamics of proteins in solution. The method presents a clear improvement with respect to coarse-grained methods based on structure potentials and opens the possibility to explore dynamics of proteins out from the equilibrium and to trace conformational changes induced by interaction of proteins with both small and macromolecular ligands.