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J Comput Chem. 2005 Jan 15;26(1):23-34.

QMQSAR: utilization of a semiempirical probe potential in a field-based QSAR method.

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  • 1Schrodinger, 120 West Forty-Fifth Street, 32nd Floor, Tower 45, New York, New York 10036-4041, USA.


A semiempirical quantum mechanical approach is described for the creation of molecular field-based QSAR models from a set of aligned ligand structures. Each ligand is characterized by a set of probe interaction energy (PIE) values computed at various grid points located near the surface of the ligand. Single-point PM3 calculations afford these PIE values, which represents a pool of independent variables from which multilinear regression models of activity are built. The best n-variable fit is determined by constructing an initial regression using standard forward stepwise selection, followed by refinement using a simulated annealing technique. The resulting fit provides an easily interpreted 3D physical model of ligand binding affinity. Validation against three literature datasets demonstrates the ability of the semiempirical potential to model critical binding interactions in diverse systems.

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