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Binding Mode Prediction for a Flexible Ligand in a Flexible Pocket using Multi-Conformation Simulated
 

Summary: Binding Mode Prediction for a Flexible Ligand in a
Flexible Pocket using Multi-Conformation Simulated
Annealing Pseudo Crystallographic Refinement
Nobuyuki Ota and David A. Agard*
Howard Hughes Medical
Institute and the Department of
Biochemistry and Biophysics
University of California at San
Francisco, San Francisco
CA 94143-0448, USA
We describe multi-conformation simulated annealing-pseudo-crystallo-
graphic re«nement (MCSA-PCR), a technique developed for predicting
the binding mode of a »exible ligand in a »exible binding pocket. To
circumvent the local-minimum problem ef«ciently, this method performs
multiple independent cycles of simulated annealing with explicit solvent,
``growing'' the ligand in the binding pocket each time. From the ensem-
ble of structures, a pseudo-crystallographic electron density map is calcu-
lated, and then conventional crystallographic re«nement methods are
used to best «t a single, optimal structure into the density map. The
advantage of the MCSA-PCR method is that it provides a direct means

  

Source: Agard, David - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collections: Biotechnology; Biology and Medicine