In silico Characterization and Docking
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Corresponding Organization :
Other organizations : West Virginia University, Kent State University
Variable analysis
- Protein structure (MAO-B 2v5z.pdb, AChE 4ey7.pdb)
- Docking software (MOE 2019)
- Ligand designation (FAD as part of the ligand set)
- Predicted logP
- Predicted total polar surface area (TPSA)
- Predicted drug likeness (Lipinski Rule of 5)
- Binding pose (most negative binding energy)
- Ligand-protein interaction (induced-fit binding mode)
- Protonation of amino acids at pH 7.4
- Binding site identified as the area where co-crystallized ligand was located
- Solvent allowed as part of the docking calculation
- Root-square mean deviation (RMSD < 2 Å) for control docking experiments
- Co-crystallized ligand
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