Difference between revisions of "FEP+ for GPCR"

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Steps for setting up a FEP prediction for membrane protein  
 
Steps for setting up a FEP prediction for membrane protein  
[[File:workflow_FEP.png|thumb|center|750px]]
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[[File:workflow_FEP.png|thumb|750px]]
  
  

Revision as of 14:39, 26 February 2021

2/25/2021 Ying Yang

Steps for setting up a FEP prediction for membrane protein

Workflow FEP.png


  • Equilibration of complex structure (with confident binding pose)

Carefully look into the binding site and make sure the residues are correctly protonated Prepare the system: build the POPC membrane, add salts, add solvent


  • Force field builder

Run force field builder for all ligands


  • Flexible ligand alignment OR core constrain docking

Depends on how similar/different are the ligands to the reference/center ligand


  • Create FEP maps


  • Write out the submission file; change host; submit on gimel5 via slurm