If a receptor is new, no data in PDB, literature regarding its active site, Should I perform blind docking??
If a receptor is new , model is in PDB, ligand bounded, then should I perform docking it those active sites where ligands were bounded (in PDB structure) or should I perform blind docking ??
or in any case should I perform site specific docking using CASTp or other active site/pocket predictor
Please help, Thanks.
Sincerely--
Sunzid.
Any docking hypothesis is better than no docking hypothesis, regardless of the source of the protein structure (experiment or prediction). Pockets can be identified with DoGSiteScorer at https://proteins.plus/
Superficial binding sites may escape automatic pocket detection if the surface is not sufficiently rugged.-- e.g., binding sites on the surface of membrane proteins in the membrane-spanning region.
After the initial docking, explore the most promising putative binding sites further by defining additional constraints to enrich docking results for poses with specific interactions.
Similar compounds will tend to bind to the same site and in similar binding mode.
Check UniProt for mutation effects and ChEMBL for activity data prior to setting up the docking. Look for common substructures in active compounds . . .
If you want to check also the allosteric site in addition to the active site
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