Validation of the use of intermolecular NOE constraints for obtaining docked structures of protein-ligand complexes
作者： MichaelJ. Gradwell , James Feeney
DOI: 10.1007/BF00190456
关键词:
摘要: The use of intermolecular NOEs for docking a small ligand molecule into its target protein has been investigated with the aim determining effectiveness and methodology this type NOE calculation. A high-resolution X-ray structure protein-ligand complex used to simulate loose distance constraints varying degrees quality, typical those estimated from experimental intensities. These simulated data were examine effect number, distribution representation on precision accuracy calculated structures. standard annealing protocol was used, as well more novel method based rigid-body dynamics. results showed some analogies similar studies complete NMR determinations, but it found that per torsion angle are required define docked structures quality. different NOE-constraint averaging methods explored benefits using 'R-6 averaging' rather than 'centre sets shown. starting in calculations obtained previous or related complex. effects conformations introducing structural differences binding site initial also considered.
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