Notes on "typical protein:ligand setup pipeline"

[jchodera]

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.

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Contributors

• John Chodera
• Julien Michel
• Peter Kasson
• Oliver Beckstein

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

What is our "typical" biomolecular preparation pipeline?

• 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

Challenges not yet addressed:

• Membrane proteins
• Proteins at surfaces/interfaces

[jchodera]

I've created a wiki version of this we can add to here.