Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized ligands are rescored with Glide or Prime mm-gb/sa or redocked and the corresponding RMSD is measured.
This workflow is derived from the work published by Paulette Greenidge from Novartis in:
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Sherman, W.; J. Chem. Inf. Model. 2014, 54(10), 2697–717
MM/GBSA binding energy prediction on the PDBbind data set: Successes, failures, and directions for further improvement. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Wolf, R.M.; J. Chem. Inf. Model. 2013, 53(1), 201–9
[Requires: Glide, LigPrep, Prime]
To use this workflow in KNIME, download it from the below URL and open it in KNIME:Download Workflow
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