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J Med Chem. 2009 May 28;52(10):3159-65. doi: 10.1021/jm801444x.

Large-scale application of high-throughput molecular mechanics with Poisson-Boltzmann surface area for routine physics-based scoring of protein-ligand complexes.

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Structural Biology, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-3500, USA.

Erratum in

  • J Med Chem. 2009 Jul 23;52(14):4549.


We apply a high-throughput formulation of the molecular mechanics with Poisson-Boltzmann surface area (htMM-PBSA) to estimate relative binding potencies on a set of 308 small-molecule ligands in complex with the proteins urokinase, PTP-1B, and Chk-1. We observe statistically significant correlation to experimentally measured potencies and report correlation coefficients for the three proteins in the range 0.72-0.83. The htMM-PBSA calculations illustrate the feasibility of procedural automation of physics-based scoring calculations to produce rank-ordered binding-potency estimates for protein-ligand complexes, with sufficient throughput for realization of practical implementation into scientist workflows in an industrial drug discovery research setting.

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