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 5YGX chain A. 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
Sequence aligned 2P4J to organisers reference structure. Extracted ligand from
the crystal structure and defined a 6A binding site around the ligand. Waters and protein atoms in the 6A grid around the co-crystal of 2P4J were used as part of the docking grid.
The 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