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Available online at www.sciencedirect.com Flexible ligand docking to multiple receptor conformations

Summary: Available online at www.sciencedirect.com
Flexible ligand docking to multiple receptor conformations:
a practical alternative
Maxim Totrov1
and Ruben Abagyan2
State of the art docking algorithms predict an incorrect binding
pose for about 5070% of all ligands when only a single fixed
receptor conformation is considered. In many more cases, lack
of receptor flexibility results in meaningless ligand binding
scores, even when the correct pose is obtained. Incorporating
conformational rearrangements of the receptor binding pocket
into predictions of both ligand binding pose and binding score
is crucial for improving structure-based drug design and virtual
ligand screening methodologies. However, direct modeling of
protein binding site flexibility remains challenging because of
the large conformational space that must be sampled, and
difficulties remain in constructing a suitably accurate energy
function. Here we show that using multiple fixed receptor
conformations, either experimentally determined by
crystallography or NMR, or computationally generated, is a


Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego


Collections: Biology and Medicine