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 will use the same protocol as described in our Nature Methods paper.

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.
Please let us know about your availability and preferences until September 30th by filling in here.