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What is Field-Based QSAR?

Field-Based QSAR is a tool for constructing a model for the relationship between known activity values and 3D characteristics of a set of aligned compounds (similar to CoMFA/CoMSIA). You can visualize the QSAR model in the Workspace to qualitatively assess where to add or remove functional groups, and use the model to quantitatively predict activities for other molecules. Additionally, you can create a scatter plot of known and predicted activities in order to evaluate the model.

The Field-Based QSAR method is an implementation of the CoMFA/CoMSIA methods with a specific set of parameters. The Lennard-Jones steric potentials are taken from the OPLS_2005 force field, as are the atomic charges for the electrostatic fields. Hydrophobic fields are based on the atom types and hydrophobic parameters in Ghose, Viswanadhan, Wendoloski, J. Phys. Chem. A 1998, 102, 3762-3772. Hydrogen bond acceptor and donor fields are based on Phase pharmacophore feature definitions, with projected points.

As the models are not exactly the same as the standard CoMFA and CoMSIA models, different names have been used in Field-Based QSAR: Force Field for CoMFA-like models, and Gaussian for CoMSIA-like models.

Note that before performing the PLS regression, scaling is applied to each field by evaluating the standard deviation in the fields at each point and then averaging the SD over all points. Each field is scaled by the ratio of the maximum of these averages over all fields to the average for the field so that a field with a large variation does not dominate over a field with a smaller variation.

Keywords: shape, electrostatics, prediction

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#1626: How can I get started with Field-Based QSAR?

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