COMP 250 |
| The accurate modeling of loops is one of the key challenges in protein structure modeling. This is especially true in cases where protein loop conformations change based upon ligand binding. Several examples are known in the literature where the size and shape of a protein binding pocket changes when comparing the Apo structure to protein complexes with diverse ligands. In this study, we examine a series of therapeutically relevant protein structures that contain loops that exhibit significant ligand-dependent conformational changes. Two methods for generating accurate loop conformations for these proteins are described; an improved protocol for induced fit docking, Sample-IFD-Refine (SIR) and a new method, Delete-Dock-Resample (DDR). |
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Poster Session
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster
Division of Computers in Chemistry |