DOI: 10.1002/jcc.540120904. Efficient search for all low energy conformations of polypeptides by Monte Carlo methods

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

10.1002/jcc.540120904

Crossref journal-article

Wiley

Journal of Computational Chemistry (311)

Abstract

AbstractThe 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.

Bibliography

von Freyberg, B., & Braun, W. (1991). Efficient search for all low energy conformations of polypeptides by Monte Carlo methods. Journal of Computational Chemistry, 12(9), 1065â1076. Portico.

Authors 2

Berthold von Freyberg (first)
Werner Braun (additional)

References 44 Referenced 104

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The source code and the documentation of the program FANTOM can be obtained from the authors.
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Dates

Type	When
Created	20 years, 7 months ago (Jan. 1, 2005, 7:38 p.m.)
Deposited	1 year, 10 months ago (Oct. 23, 2023, 3:06 a.m.)
Indexed	4 days, 11 hours ago (Aug. 20, 2025, 8:32 a.m.)
Issued	33 years, 9 months ago (Nov. 1, 1991)
Published	33 years, 9 months ago (Nov. 1, 1991)
Published Online	20 years, 11 months ago (Sept. 7, 2004)
Published Print	33 years, 9 months ago (Nov. 1, 1991)

Funders 0

None

BibTeX

@article{von_Freyberg_1991, title={Efficient search for all low energy conformations of polypeptides by Monte Carlo methods}, volume={12}, ISSN={1096-987X}, url={http://dx.doi.org/10.1002/jcc.540120904}, DOI={10.1002/jcc.540120904}, number={9}, journal={Journal of Computational Chemistry}, publisher={Wiley}, author={von Freyberg, Berthold and Braun, Werner}, year={1991}, month=nov, pages={1065–1076} }

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