The effect of region size on CoMFA analyses

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Medicinal Chemistry Research


The Comparative Molecular Field Analysis method of QSAR requires the generation of three-dimensional grid surrounding molecular structures under investigation. The quality of the final QSAR equation is conventionally characterized by the value of cross-validated R2 (q2). We discuss the effects of the grid size on the value of q2. Previous studies that have focused on the effect of grid spacing and lattice position have been inconclusive as to whether changes in grid size affect greatly the calculated q2. We show that in the original CoMFA program implemented in Tripos, Inc. Sybyl software, the grid spacing is inconsistent in that it depends on the size of the region and that changing the dimensions of the region can affect the value of q2 dramatically. Scientists using CoMFA as a standard QSAR tool should take this characteristic of the CoMFA software into account when performing analyses.

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