I just wanted to repost the notes on what goes into a "typical protein:ligand setup pipeline" from our meeting at MolSSI on 8 Oct 2016.

Contributors

Before starting, Julien frequently does some manual inspection in a GUI:

missing loops
incomplete residues
cofactors: keep or discard? where to get parameters?
ions: keep or substitute?
crystal waters: keep or throw away?
crystal contacts, domain swapping
Read PDB paper to ensure that this is the protein structure that he wants to use
Note that assay conditions may differ from crystallographic conditions

Decide which structure you want to use
Decide which chain to use if multiple copies
Reverting mutations or simulate a different construct
Disulfide if not in a reducing environment
Address PTMs
Julien typically uses the Maestro Protein Prep Wizard to:
- add missing loops (up to a certain length)
- add N/C-termini? Most people omit these
- assign protonation states for desired pH
- keep crystal waters; add hydrogens
- interactively check histidine
Structural metal ions (e.g. Zn2+, Ca2+):
- decide whether to retain
- substitute with multisite models (alternatives: covalently bonded (harmonically restrained); single-site LJ)
Ligands and cofactors:
- pick protonation state / tautomer
- find or create parameters
- covalently bound cofactors?
- Consult Uppsala EDS to verify that ligand density justifies binding mode
- model in rest of ligand or replace the ligand with another one (CCSD? swap from other PDB file? OpenEye)
Protonation states?
- (PROPKA? 3.1 can do ligands; MCCE2?) Counterions and solvent
- can do in either order
- how big should box be? what shape? what buffer should be used? (Peter Kasson uses 20A buffer; Julien uses 12A; Oliver uses 15A)
- for membrane proteins, at least 3-4 layers of lipids sideways; z-axis is very tricky
- ionic strength