MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.
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.
Joint IRB-BSC Computational Biology Programme, Institute of Research in Biomedicine, Parc Científic de Barcelona, Baldiri Reixac 10, Barcelona 08028, Spain.
Tim
T
Meyer
Marco
M
D'Abramo
Adam
A
Hospital
Manuel
M
Rueda
Carles
C
Ferrer-Costa
Alberto
A
Pérez
Oliver
O
Carrillo
Jordi
J
Camps
Carles
C
Fenollosa
Dmitry
D
Repchevsky
Josep Lluis
JL
Gelpí
Modesto
M
Orozco
D057225:Data Mining; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012984:Software; D012997:Solvents / Q000737:chemistry
D012997:Solvents