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Marcel Schumann and Roger S. Armen Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure Journal of Computational Chemistry 34

Version of Record online: 19 FEB 2013 | DOI: 10.1002/jcc.23251

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Modeling receptor side chain flexibility is important for molecular docking, as it allows the receptor to adopt new conformations as induced by ligand binding. A new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers is described. The approach is validated using the 40 DUD target benchmarks, and large improvement is demonstrated using the developed side chain optimization over rigid receptor docking.

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