Use case: HSP90 #6
Description
Attachment
Input:
HSP90.txt
smiles.txt
Output:
[PDB1-4]-HSP90_40-1.pdb[inpcrd/prmtop]
Setup description
This workflow takes variability in available crystal structures into account. HSP90 was part of the D3R 2015 Grand Challenge. There are a large number of crystal structures available on the PDB. This workflow has the challenge to on top of coming up with a reasonable binding pose to also select a pdb structure. The idea is to cluster available PDBs, e.g. using RMSD and spectral clusters to then find representative structures in each cluster center and use these as a basis for docking. Then each compound in smiles.txt is docked to all selected protein clusters, ideally from then on following the use case description of issue #5.
Attached are the pdb structures with an example ligand docked using rDock and the top scoring pose. For maximal usefulness a set of inputrcd and prmtop files should be generated rather than just the pdb structures. The ligand should then be paramatrised using a default protocol, e.g AM1-BCC charges including an automated forcefield selection for the protein followed by solvation in a water box specifying a given water model. All this while taking care of protonation states and appropriate neutralisation using counter ions.