Protein-ligand docking has become a commonly used method for lead identification and refinement, primarily due to the increase in availability of high-quality structural information. Traditionally, structure-based docking methods have represented the receptor as a rigid body, but have recently been trending towards incorporating protein flexibility. Proteins exist in an inter-converting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method within CHARMM. This method incorporates side chain flexibility with grid-based docking methods, maintaining efficiency while still allowing the protein and ligand configurations to explore their conformational space simultaneously. Presented here are docking results from re-docking and assessment of the benefits of including protein flexibility when compared with traditional rigid docking methods.

Flexible CDOCKER: Development and application of a docking method incorporating non-rigid receptors within CHARMM

249th National Meeting (2015)

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