On the approximation of protein threading
Conference
·
OSTI ID:548990
- Univ. of Tokyo (Japan)
In this paper, we study the protein threading problem, which was proposed for finding a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard by Lathrop, we study polynomial time approximation algorithms. First we show that the protein threading problem is MAX SNP-hard. Next we show that the protein threading problem can be approximated within a factor 4 for a special case in which a graph representing interaction between residues (amino acids) is planar. This case corresponds to a {beta}-sheet substructure, which appears in most protein structures. 14 refs., 9 figs.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 548990
- Report Number(s):
- CONF-970137--
- Country of Publication:
- United States
- Language:
- English
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