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| - A QXP-Based Multistep Docking Procedure for Accurate Prediction of Protein−LigandComplexes
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| - The two great challenges of the docking process are the prediction of ligand poses in a protein binding siteand the scoring of the docked poses. Ligands that are composed of extended chains in their molecularstructure display the most difficulties, predominantly because of the torsional flexibility. On the basis of themolecular docking program QXP-Flo+0802, we have developed a procedure particularly for ligands witha high degree of rotational freedom that allows the accurate prediction of the orientation and conformationof ligands in protein binding sites. Starting from an initial full Monte Carlo docking experiment, this wasachieved by performing a series of successive multistep docking runs using a local Monte Carlo searchwith a restricted rotational angle, by which the conformational search space is limited. The method wasestablished by using a highly flexible acetylcholinesterase inhibitor and has been applied to a number ofchallenging protein−ligand complexes known from the literature.
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