2020-08-11 PLBenchmarks Meeting notes

Content

• CB: valid benchmark set:

  • what’s the protein? → identity (EC number)

  • what are the ligands? → smiles

  • what are the activities?

  • everything else is an interpretation. (methods, ff, poses, charges, ….)

• Stages

  1. above data

  2. + structures (PDB + poses)

  3. + partial charges, FF parameters

  4. method, method parameters

• Ligands:

  • Structure as sdf file

    • coordinates

    • partial charges?

    • activity?

    • reference?

  • Charges (CB: if you want to evaluate e.g. another pose, we want to keep the charges constant)

• Protein:

  • Structure as pdb file (protein.pdb + all other crystal molecules in <find_a_name>.pdb)

    • generated with gromacs gmx pdb2gmx

    • <find_a_name> : ‘water+other’, ‘water+cofactors’, ‘other’?

• Hybrid:

  • hybrid struct based on ligand A

  • hybrid struct based on ligand B

• Problems with current version:

  • partial charges

  • boxes (dimensions, number of mols)

  • position of waters and ions

File types

• GC: very Gromacs centric

• Is the sdf format lossless?

  • no, e.g. B-factor information are lost

Remaining questions

• Is there a general format/presentation for chimeric molecules? (GC: look in FEsetup), CB: unique naming of atoms might be useful: OETriposAtomNames

• Do we provide (Gromacs) topologies?