Efficient search for all low energy conformations of polypeptides by Monte Carlo methods

Berthold von Freyberg, Werner Braun

Research output: Contribution to journalArticle

97 Citations (Scopus)

Abstract

The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met‐enkephalin. In total, 1881 conformations below −10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root‐mean‐square‐deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below −10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.

Original languageEnglish (US)
Pages (from-to)1065-1076
Number of pages12
JournalJournal of Computational Chemistry
Volume12
Issue number9
DOIs
StatePublished - 1991
Externally publishedYes

Fingerprint

Polypeptides
Conformation
Monte Carlo method
Conformations
Monte Carlo methods
Peptides
Energy
Global Minimization
Newton-Raphson
Hydrogen Bonds
Global Minimum
Backbone
Energy Function
Minimizer
Local Minima
Torsional stress
Torsion
Pairwise
Hydrogen bonds
Schedule

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Efficient search for all low energy conformations of polypeptides by Monte Carlo methods. / von Freyberg, Berthold; Braun, Werner.

In: Journal of Computational Chemistry, Vol. 12, No. 9, 1991, p. 1065-1076.

Research output: Contribution to journalArticle

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