title: United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials.
abstract: We present a method for the efficient simulation of the equilibrium dynamics of proteins based on the well established discrete molecular dynamics algorithm, which avoids integration of Newton equations of motion at short time steps, allowing then the derivation of very large trajectories for proteins with a reduced computational cost. In the presented implementation we used an all heavy-atoms description of proteins, with simple potentials describing the conformational region around the experimental structure based on local physical interactions (covalent structure, hydrogen bonds, hydrophobic contacts, solvation, steric hindrance, and bulk dispersion interactions). The method shows a good ability to describe the flexibility of 33 diverse proteins in water as determined by atomistic molecular dynamics simulation and can be useful for massive simulation of proteins in crowded environments or for refinement of protein structure in large complexes.
authors.affiliation: Joint IRB-BSC research program in Computational Biology, Institute for Research in Biomedicine (IRB), Josep Samitier 1-5, Barcelona 08028, Spain, Barcelona Supercomputing Centre (BSC), Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Agustí
authors.initials: A
authors.lastname: Emperador
authors.affiliation: Joint IRB-BSC research program in Computational Biology, Institute for Research in Biomedicine (IRB), Josep Samitier 1-5, Barcelona 08028, Spain, Barcelona Supercomputing Centre (BSC), Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Tim
authors.initials: T
authors.lastname: Meyer
authors.affiliation: Joint IRB-BSC research program in Computational Biology, Institute for Research in Biomedicine (IRB), Josep Samitier 1-5, Barcelona 08028, Spain, Barcelona Supercomputing Centre (BSC), Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco