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MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories
ISSN
0969-2126
Date Issued
2010-11-10
Author(s)
D'Abramo, Marco
Hospital, Adam
Rueda, Manuel
Ferrer-Costa, Carles
Pérez, Alberto
Carrillo, Oliver
Camps, Jordi
Fenollosa, Carles
Repchevsky, Dmitry
Gelpí, Josep Lluis
Orozco, Modesto
DOI
10.1016/j.str.2010.07.013
Abstract
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.