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Virtual Screening

Virtual Screening. protein-ligand interactions, inhibitors, SBDD kinetics, competitive, slow, aggregators H-bonding, halogens, co-factors, metal ions chemi-informatics tanimoto similarity, clustering Lipinski’s rules predicting solubility, aggregation

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Virtual Screening

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  1. Virtual Screening • protein-ligand interactions, inhibitors, SBDD • kinetics, competitive, slow, aggregators • H-bonding, halogens, co-factors, metal ions • chemi-informatics • tanimoto similarity, clustering • Lipinski’s rules • predicting solubility, aggregation • 3D conformational sampling (but not rings); ROCS • pharmacophore search • QSAR, GRID • screening • docking algorithms, scoring functions

  2. screening • docking algs: anchor-and-grow, ICM, Monte Carlo • receptor flexibility (dof, MD) • partial charges, tautomers • solvation energy • entropy • mining minima (Gilson and Zhou, 2007) • -0.4..-1 kcal/mol/rotbond • LUDI/Chemscore • PMF • consensus scoring, LIE

  3. Induced Fit • James and Tawfik (PNAS, 2005) • IgE antibody binds many ligands promiscuously, but only a few specifically and tightly • anthrone (2BJM) vs. alizarin red (1OAR) • involves secondary isomerization, movement of Tyr in H3 loop by 14A to grasp ligand tighter • multiple phases/rates in pre-steady state kinetics

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