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Summary: Large-Scale Prediction of Protein Geometry and Stability
Changes for Arbitrary Single Point Mutations
A. J. Bordner1,2* and R. A. Abagyan1,2
1
The Scripps Research Institute, 10550 North Torrey Pines Rd., Mail TPC-28, San Diego, California
2
Molsoft LLC, 3366 North Torrey Pines Court, Suite 300, San Diego, California
ABSTRACT We have developed a method to
both predict the geometry and the relative stability
of point mutants that may be used for arbitrary
mutations. The geometry optimization procedure
was first tested on a new benchmark of 2141 ordered
pairs of X-ray crystal structures of proteins that
differ by a single point mutation, the largest data set
to date. An empirical energy function, which in-
cludes terms representing the energy contributions
of the folded and denatured proteins and uses the
predicted mutant side chain conformation, was fit
to a training set consisting of half of a diverse set of
1816 experimental stability values for single point
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