Flare_docking
Flare 2.0.0 Revision 34140
pH= 4.5
Download 2P4J within Flare, delete all chains, ligands, and waters other than those of chain A. Align to BA01-BA20 as given by the organisers. Use the protein prep wizard in Flare to clean the protein assign protonation states to amino acids and cap ends.
Grid definition: 6A around ligand found in 2P4J including water molecules.
Quality: normal
Max Poses: 1
Pool Size: 1.00
Population Size: 1.00
Minimize Ligands before Docking: Yes
Rotate Amide Bonds: yes
Rotate Ester Bonds: Yes
Rotate Conjugated Bonds: Heuristically
Protein 2P4J was aligned with reference structures. Extracted ligand from protein 2P4J and defined docking grid for proteins BA01-BA20 based on ligand from 2P4J. In each co-crystal structure all water molecules were retained. Each BA01-20 protein was prepared using the protein prepare option of Flare, capping the terminal amino acids and protonate according to a pH of 4.5. Ligands were read in in smiles format. Using the docking button a docking calculations of all ligands were carried out with the following options: The quality was set to 'normal', only one pose was retained with a pool size of 1.00 and a population size of 1.00. Ligands were minimised before docking and amide and ester bonds were allowed to be rotated. The rotation of conjugated bond was done heuristically.
no
yes