Tuesday, January 30, 2018

Database of the NMRlipids simulations and experiments

As a byproduct of its scientific findings, the NMRlipids project has generated the largest publicly available collection of molecular dynamics simulation data. Most of the raw data (i.e. trajectories) are available at the NMRlipids Zenodo community, whereas the analyzed data can be found in the GitHub repositories, as catalogued in the tables of our publications (NMRlipids I, NMRlipids IINMRlipids III, and NMRlipids IV).

We have now catalogued these data also in an SQL database, available at www.nmrlipids.fi.

In the future we plan to extend the database with automatic force field quality assessment tools (demo version already available for Berger POPC system), as well as add other than lipid bilayer systems. We believe that such a database will be useful for force field development, as well as for choosing the most suitable force field for a given application.

The current database is essentially just a search engine for the MATCH repository of the NMRlipids GitHub organization. Thus indexing follows the folder structure of MATCH, and links to the corresponding MATCH folders are given. Note that both experimental data (through the links in the Temperature column) and simulation data (Modelfiles column) are available.

As said, the database is open for extensions. For example, currently it still lacks some of the data from the NMRlipids publications. We warmly welcome you to fork the GitHub repository, add your data in the appropriate folder, and make a pull request. We are also exploring options to write a peer reviewed publication describing the database (and the automatic quality assessment protocol). However, we are currently fully employed by the NMRlipids III and NMRlipids IV projects, as well as with other commitments. Hence, should you be interested in facilitating the database activity, please let us know.

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