Springer Protocols: Abstract: Predictive Models of Protein-Active Sites

Predictive Models of Protein-Active Sites

By: D. Eric Walters²

Abstract

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For many proteins, we do not have enough information to even attempt to predict the three-dimensional (3D) structure. Many drug receptors, e.g., are membrane-bound proteins for which there is not a crystal structure of any homologous protein available. But drug receptors are proteins for which it would be especially useful to know the 3D structure. Fortunately for the drug design problem, it is often sufficient to be able to construct a reasonable model of the receptor protein’s active site, and there are several ways in which we can construct such models. In this chapter we consider two approaches to constructing binding-site models. Both of these use a common starting point: a series of ligands for which binding (or other biological activity) has been measured. This structure-activity series serves as a template around which the active site model is built. The two methods differ only in the ways in which the binding site is represented (graphical surface or atoms).

Affiliation(s): (2) Department of Biological Chemistry, Finch University of Health Sciences, The Chicago Medical School, North Chicago, IL

Book Title: Protein Structure Prediction: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 143 | Pub. Date: Aug-15-2000 | Page Range: 349-358 | DOI: 10.1385/1-59259-368-2:349

Subject: Protein Science

References

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