On the approximation of protein threading

Conference · Mon Dec 01 00:00:00 EST 1997

OSTI ID:548990

Akutsu, Tatsuya; Miyano, Satoru ^[1]

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1. 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-; TRN: 97:005298-0002
• Resource Relation: Conference: RECOMB `97: 1. annual conference on research in computational molecular biology, Santa Fe, NM (United States), 20-22 Jan 1997; Other Information: PBD: 1997; Related Information: Is Part Of RECOMB 97. Proceedings of the first annual international conference on computational molecular biology; PB: 370 p.
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 MATHEMATICS
COMPUTERS
INFORMATION SCIENCE
MANAGEMENT
LAW
MISCELLANEOUS
STRUCTURAL MODELS
ALGORITHMS
PROTEIN STRUCTURE
MATHEMATICAL MODELS
TOPOLOGICAL MAPPING
PROTEINS
AMINO ACID SEQUENCE
STRUCTURE-ACTIVITY RELATIONSHIPS
AMINO ACIDS
CONFIGURATION INTERACTION
MOLECULAR BIOLOGY
POLYNOMIALS