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Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16041-6. Epub 2002 Dec 2.

The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds.

Author information

1
Department of Chemistry and Biochemistry, and University of California, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095-1570, USA.

Abstract

The Directional Atomic Solvation EnergY (DASEY) is an atom-based description of the environment of an amino acid position within a known 3D protein structure. The DASEY has been developed to align and score a probe amino acid sequence to a library of template protein structures for fold assignment. DASEY is computed by summing the atomic solvation parameters of atoms falling within a tetrahedral sector, or petal, extending 16 A along each of the four bond axes of each alpha-carbon atom of the protein. The DASEY discriminates between pairs of structurally equivalent positions and random pairs in protein structures sharing a fold but belonging to different superfamilies, unlike some previous descriptors of protein environments, such as buried area. Furthermore, the DASEY values have characteristic patterns of residue replacement, an essential feature of a successful fold assignment method. Benchmarking fold assignment with DASEY achieves coverage of 56% of sequences with 90% accuracy when probe sequences are matched to protein structural templates belonging to the same fold but to a different superfamily, an improvement of greater than 200% over a previous method.

PMID:
12461172
PMCID:
PMC138561
DOI:
10.1073/pnas.252626399
[Indexed for MEDLINE]
Free PMC Article
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