BioSimGrid: towards a worldwide repository for biomolecular simulations.
BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.
Tai
Kaihsu
K
Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. team@BioSimGrid.org
Murdock
Stuart
S
Wu
Bing
B
Ng
Muan Hong
MH
Johnston
Steven
S
Fangohr
Hans
H
Cox
Simon J
SJ
Jeffreys
Paul
P
Essex
Jonathan W
JW
Sansom
Mark S P
MS
D000110:Acetylcholinesterase / Q000737:chemistry / Q000378:metabolism; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D010740:Phospholipases / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D040681:Structural Homology, Protein; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry / Q000378:metabolism
D001425:Bacterial Outer Membrane Proteins; D011506:Proteins; D013762:Tetrahydrofolate Dehydrogenase; D010740:Phospholipases; D000110:Acetylcholinesterase