More than 1,700 trajectories of proteins representative of all monomeric soluble structures in PDB have been studied by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. Trajectories and analysis performed on them are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. This web site is the main entry point to the library, showing the simulated structures, and basic, pre-made, analysis on them. The web site is in constant update, not only on the simulations available, but also on the analysis and tools included.
MoDEL is a product of years of experience of our group in the preparation, simulation and analysis of molecular dynamics trajectories. People and institutions involved follows:
Josep Lluis Gelpí
|Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028. Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona. Barcelona 08034, Spain
National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028. Spain and Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona. Barcelona 08034, Spain
Departament de Bioquímica i Biología Molecular, Facultat de Biología, Avgda Diagonal 645, Barcelona 08028, Spain
T. Meyer, M. D'Abramo, A. Hospital, M. Rueda, C. Ferrer-Costa, A. Pérez, O. Carrillo, J. Camps, C. Fenollosa, D. Repchevsky, J. Ll. Gelpí and M. Orozco. MoDEL (Molecular Dynamics Extended Library): A database of atomistic molecular dynamics trajectories. (2010) Structure (in press)