skip to main content

Title: Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

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,more » 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.« less
Authors:
 [1] ;  [2] ;  [3]
  1. National Institutes of Health, Bethesda, MD (United States)
  2. MIT Lab. for Computer Science, Cambridge, MA (United States)
  3. Univ. of Southern California, Los Angeles, CA (United States) [and others
Publication Date:
OSTI Identifier:
548989
Report Number(s):
CONF-970137--
TRN: 97:005298-0001
Resource Type:
Conference
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.
Publisher:
Association for Computing Machinery, New York, NY (United States)
Research Org:
Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, 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