Search for the stable state of a short chain in a molecular field

Protein Eng. 1992 Oct;5(7):617-24. doi: 10.1093/protein/5.7.617.

Abstract

A general approach is developed to search for stable structures of short chain fragments (e.g. of loops or bound oligopeptides) in a given molecular field. This molecular field is produced by the remaining part of a globule or by any other surface with a defined spatial structure. The fragment must be short enough to have no pronounced long-range interactions within itself. The method is illustrated by calculation of the 3-D structures of two loops of bovine pancreatic trypsin inhibitor (BPTI). Computations are based on a lattice model of conformational space and on strict and fast algorithms of 1-D statistical mechanics and dynamic programming (which are very similar in essence). This makes a search of oligopeptide structures only several times (and not several orders of magnitude) longer than that of a dipeptide.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Aprotinin / chemistry*
  • Mathematical Computing
  • Models, Chemical*
  • Models, Molecular
  • Peptide Fragments / chemistry
  • Protein Folding*
  • Software

Substances

  • Peptide Fragments
  • Aprotinin