The main goal of Limonada ("Lipid Membrane Open Network And Database") is to provide an online library of membranes, notably of more complex compositions representative of biological membranes, along with the description of lipids, topologies and forcefields mandatory for their molecular dynamics simulations.
Limonada uses the lipid classification established by the LipidMaps consortium and every lipid is unequivocally identified by a four-digit ID (i.e. compliant with e.g. pdb files). From this basis, registered users can add new membranes, lipids, topologies and/or forcefields to the database with the only limitation that each addition must be sustained by a reference paper and that the primary source of the files stored by Limonada are also provided.
At creation, membrane composition, lipid and reference forms can be filled by giving a membrane structure file, a LipidMaps ID and a DOI, respectivelly. Topology files are validated according to the specified forcefield and software and the membrane composition according to the membrane structure file. Simulation files for a given membrane record can then automatically be gathered and downloaded from the database.
Limonada is open source (code is hosted on github: https://github.com/limonadaMD) and is built using the widely used Django open framework (https://www.djangoproject.com).
The size and complexity of lipid systems simulated by molecular dynamics is continuously growing and knowing that there could be over 100,000 lipid species and that biological membranes can be composed by hundreds of different lipids whose proportion are organism and organelle specific, the amount and complexity of the data involved stress the need for an organized open web database.
Indeed, several forcefields can be used for lipid membrane simulations and some of them have hundreds of different lipid topologies parametrized. Moreover, tens of model membranes with several lipid species designed to represent specific biological membranes have already been simulated. Modeling studies start then to encompass the wide diversity of biological membranes. Besides, determination of complex lipid compositions is not trivial and their equilibration can be quite computationally demanding while only being a prerequisite for further simulations.