Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model
- National Institutes of Health, Bethesda, MD (United States)
- MIT Lab. for Computer Science, Cambridge, MA (United States)
- Univ. of Southern California, Los Angeles, CA (United States); and others
A long standing problem in molecular biology is to determine the three-dimensional structure of a protein, given its amino acid sequence. A variety of simplifying models have been proposed abstracting only the {open_quotes}essential physical properties{close_quotes} of real proteins. In these models, the three dimensional space is often represented by a lattice. Residues which are adjacent in the primary sequence (i.e. covalently linked) must be placed at adjacent points in the lattice. A conformation of a protein is simply a self-avoiding walk along the lattice. The protein folding problem STRING-FOLD is that of finding a conformation of the protein sequence on the lattice such that the overall energy is minimized, for some reasonable definition of energy. This formulation leaves open the choices of a lattice and an energy function. Once these choices are made, one may then address the algorithmic complexity of optimizing the energy function for the lattice. For a variety of such simple models, this minimization problem is in fact NP-hard. In this paper, we consider the Hydrophobic-Polar (HP) Model introduced by Dill. The HP model abstracts the problem by grouping the 20 amino acids into two classes: hydrophobic (or non-polar) residues and hydrophilic (or polar) residues. For concreteness, we will take our input to be a string from (H,P){sup +}, where P represents polar residues, and H represents hydrophobic residues. Dill et.al. survey the literature analyzing this model. 8 refs., 2 figs., 1 tab.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 548989
- Report Number(s):
- CONF-970137-; TRN: 97:005298-0001
- 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
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Related Subjects
BASIC STUDIES
99 MATHEMATICS
COMPUTERS
INFORMATION SCIENCE
MANAGEMENT
LAW
MISCELLANEOUS
PROTEINS
AMINO ACID SEQUENCE
PHYSICAL PROPERTIES
STRUCTURE-ACTIVITY RELATIONSHIPS
STRUCTURAL MODELS
ELECTRONIC STRUCTURE
TWO-DIMENSIONAL CALCULATIONS
THREE-DIMENSIONAL CALCULATIONS
ALGORITHMS
S CODES
POLAR COMPOUNDS
COVALENCE
PROTEIN STRUCTURE
COMPUTERIZED SIMULATION
MOLECULAR BIOLOGY
ENERGY LEVELS