MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.
|Title||MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.|
|Publication Type||Journal Article|
|Year of Publication||2010|
|Authors||Meyer, Tim, D’Abramo Marco, Hospital Adam, Rueda Manuel, Ferrer-Costa Carles, Pérez Alberto, Carrillo Oliver, Camps Jordi, Fenollosa Carles, Repchevsky Dmitry, Gelpí Josep-Lluis, and Orozco Modesto|
|Date Published||2010 Nov 10|
|Keywords||Data Mining, Databases, Internet, Models, Molecular, Molecular Dynamics Simulation, Protein, Protein Conformation, Software, Solvents|
More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. The trajectories and analyses are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. Here, we describe the project and the structure and contents of our database, and provide examples of how it can be used to describe the global flexibility properties of proteins. Basic analyses and trajectories stripped of solvent molecules at a reduced resolution level are available from our web server.