DOI: 10.1002/prot.340140111. Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space

Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space

10.1002/prot.340140111

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractA new minimization procedure for the global optimization is cartesian coordinate space of the conformational energy of a polypeptide chain is presented. The Metropolis Monte Carlo minimization is thereby supplemented by a thermalization process, which is initiated whenever a structure becomes trapped in an area containing closely located local minima in the conformational space. The method has been applied to the endogenous opioid pentapeptide methionine enkephalin. Five among 13 different starting conformations led to the same apparent global minimum of an in‐house developed energy function, a type II′ reverse turn, the central residues of which are Gly‐3‐Phe‐4. A comparison between the ECEPP/2 global minimum conformation of methionine enkephalin and the apparent one achieved by the present method shows that minimum‐energy conformations having a certain similarity can be generated by relatively different force fields. © 1992 Wiley‐Liss, Inc.

Bibliography

Caflisch, A., Niederer, P., & Anliker, M. (1992). Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space. Proteins: Structure, Function, and Bioinformatics, 14(1), 102â109. Portico.

Authors 3

Amedeo Caflisch (first)
Peter Niederer (additional)
Max Anliker (additional)

References 12 Referenced 26

10.1073/pnas.47.9.1309
10.1096/fasebj.4.14.2227210 / FASEB / Theoretical studies of protein conformation by means of energy computations by Némethy G. (1990)
{'key': 'e_1_2_1_4_2', 'first-page': '3', 'article-title': 'Calculations of stable conformations of polypeptides, proteins, and protein complexes', 'volume': '29', 'author': 'Scheraga H. A.', 'year': '1989', 'journal-title': 'Chem. Scripta'} / Chem. Scripta / Calculations of stable conformations of polypeptides, proteins, and protein complexes by Scheraga H. A. (1989)
10.1073/pnas.84.19.6611
10.1016/0166-1280(88)80133-7
10.1021/j100589a006
10.1021/j100234a011
Caflisch A.Monte Carlo‐docking of polypeptide chains; a general model with applications to oligopeptides bonded to class I MHC proteins. Ph. D. thesis ETH Zürich 1991. ETH diss 9400.
10.1002/prot.340130305
10.1002/jcc.540040211
10.1063/1.1699114
10.1016/0022-2836(87)90041-6

Dates

Type	When
Created	20 years, 3 months ago (May 28, 2005, 9:20 p.m.)
Deposited	1 year, 10 months ago (Oct. 23, 2023, 3:40 p.m.)
Indexed	3 months ago (June 5, 2025, 7:47 a.m.)
Issued	33 years ago (Sept. 1, 1992)
Published	33 years ago (Sept. 1, 1992)
Published Online	21 years, 7 months ago (Feb. 3, 2004)
Published Print	33 years ago (Sept. 1, 1992)

Funders 0

None

BibTeX

@article{Caflisch_1992, title={Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space}, volume={14}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.340140111}, DOI={10.1002/prot.340140111}, number={1}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Caflisch, Amedeo and Niederer, Peter and Anliker, Max}, year={1992}, month=sep, pages={102–109} }

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