Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins
Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1222-1231, 2003
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 24(2003), 10 vom: 30. Juli, Seite 1222-31 |
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| Weitere Verfasser: | , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2003
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Peptides Proteins Aprotinin 9087-70-1 Ribonuclease, Pancreatic EC 3.1.27.5 |
| Zusammenfassung: | Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1222-1231, 2003 Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited-memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computat Opt Appl 2002, 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all-atom AMBER force field with a dielectric constant epsilon = 1 and a distance-dependent dielectric function epsilon = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from epsilon = 2r to epsilon = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial-and-error calculations for each problem |
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| Beschreibung: | Date Completed 11.02.2004 Date Revised 14.11.2007 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |