Computational protocol: The Impactof Introducing a Histidine into an ApolarCavity Site on Docking and Ligand Recognition

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Protocol publication

[…] Crystals were grown as previously described. Crystals were placed in the cryo solution containing enough of each ligand to make a 5 mM ligand solution and soaked overnight at 4 °C. An initial set of molecules expected to bind was used as an initial crystallographic screening test set (). Data sets were obtained at the ALS beamline 8.3.1 and have been deposited in the PDB (). Reflections were integrated and scaled with XDS. Molecular replacement was performed with PHASER. Models were refined initially using simulated annealing using PHENIX and COOT and later were refined with TLS B-factors. Ligand parameters were generated using PRODRG. Complex structures were solved by molecular replacement using the structure of L99A/M102H† in complex with 2-mercaptoethanol. The models were checked with MolProbity. Figures were made with PyMOL. RMSD values were calculated between the crystal and DOCK poses manually; when discernible specific atoms were identified, although in cases of significant degeneracy (e.g., benzene) distances were measured between the nearest possibly correct atom. […]

Pipeline specifications

Software tools XDS, PHENIX, Coot, PRODRG, MolProbity, PyMOL
Applications Drug design, Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma