title: Post-docking optimization and analysis of protein-ligand interactions of estrogen receptor alpha using AMMOS software.
abstract: 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.
authors.affiliation: University Paris Diderot, Sorbonne Paris Cite, Paris, France. maria.miteva@univ-paris-diderot.fr
authors.forename: Tania
authors.initials: T
authors.lastname: Pencheva
authors.forename: Dessislava
authors.initials: D
authors.lastname: Jereva
authors.forename: Maria A
authors.initials: MA
authors.lastname: Miteva
authors.forename: Ilza
authors.initials: I
authors.lastname: Pajeva
mesh_terms: D018360:Crystallography, X-Ray; D047628:Estrogen Receptor alpha / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D012984:Software
chemical_list: D047628:Estrogen Receptor alpha; D008024:Ligands