Second simulation round
After our first successful publication in Nature Methods, we are back to increase the data coverage of GPCRmd in a 2nd simulation round, starting in October 2020.
In this round, we will focus on simulating all remaining PDB IDs which correspond to GPCRs which are not in complex with G proteins, arrestins, or nanobodies. Note that GPCR-G protein/arrestin/nanobody complexes will be addressed in the 3rd simulation round starting in January 2021.
The time schedule for the 2nd simulation round is the following:
- October 2020: Receptor curation*
- November 2020: System setup*
- December 2020 - January 2021: Equilibration and production runs*
- February 2021: Data analysis
- March 2021: Manuscript preparation
We are looking for support for two parts:
Part 1 (basic contribution - main GPCRmd community paper):
- Support for receptor curation of your receptors of interest
- Quality check for equilibration and production runs
Part 2 (additional contribution - spin-off papers by contributors):
- Propose different simulation conditions to address a scientific problem (e.g. different ligand, membrane composition, mutation).
- Compare different simulation engines, force fields, and system setups.
- Other ideas.