Post-docking optimization and analysis of protein-ligand interactions of estrogen receptor alpha using AMMOS software.
2013
Understanding protein-ligand interactions is a critical step in rational drug design/virtual ligand screening. In
this work we applied the AMMOS_ProtLig software for post-docking optimization of estrogen receptor alpha complexes
generated after virtual ligand screening protocol. Using MOE software we identified the ligand-receptor interactions in the
optimized complexes at different levels of protein flexibility and compared them to the experimentally observed
interactions. We analyzed in details the binding sites of three X-ray complexes of the same receptor and identified the key
residues for the protein-ligand interactions. The complexes were further processed with AMMOS_ProtLig and the
interactions in the predicted poses were compared to those observed in the X-ray structures. The effect of employing
different levels of flexibility was analyzed. The results confirmed the AMMOS_ProtLig applicability as a helpful postdocking
optimization tool for virtual ligand screening of estrogen receptors.
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