The MDDB (Molecular Dynamics Data Bank) project is an initiative to collect, preserve, and share molecular dynamics (MD) simulation data. As part of this project, MDposit is an open platform that provides web access to atomistic MD simulations. Its goal is to facilitate and promote data sharing within the global scientific community to advance research.
The MDposit infrastructure is distributed across several MDposit nodes. All metadata are accessible through the global node:
MDposit MMB node:
- web site: https://mdposit.mddbr.eu/
- documentation: https://mdposit.mddbr.eu/#/help
- API: https://mdposit.mddbr.eu/api/rest/docs/
- API base URL: https://mdposit.mddbr.eu/api/rest/v1
No account / token is needed to access the MDposit API.
In MDposit, a dataset (a simulation and its related files) is called a "project".
API entrypoint to get the total number of projects:
- Endpoint:
/projects/summary - HTTP method: GET
- documentation
A project can contain multiple replicas, each identified by project_id.replica_id.
For example, the project MD-A003ZP contains ten replicas:
MD-A003ZP.1: https://mdposit.mddbr.eu/#/id/MD-A003ZP.1/overviewMD-A003ZP.2: https://mdposit.mddbr.eu/#/id/MD-A003ZP.2/overviewMD-A003ZP.3: https://mdposit.mddbr.eu/#/id/MD-A003ZP.3/overview- ...
API entrypoint to get all datasets at once:
- Endpoint:
/projects - HTTP method: GET
- documentation
API endpoint to get files for a given replica of a project:
- Endpoint:
/projects/{project_id.replica_id}/filenotes - HTTP method: GET
- documentation
Title:
MDBind 3x1k
Description:
10 ns simulation of 1ma4m pdb structure from MDBind dataset, a dynamic view of the PDBBind database
Files for replica 1:
Title:
All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C4 popc
Description:
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
Files for replica 1: