Efficiency of monte carlo minimization procedures and their use in analysis of NMR data obtained from flexible peptides
Article first published online: 7 DEC 1998
Copyright © 1997 John Wiley & Sons, Inc.
Journal of Computational Chemistry
Volume 18, Issue 2, pages 240–253, 30 January 1997
How to Cite
Meirovitch, H. and Meirovitch, E. (1997), Efficiency of monte carlo minimization procedures and their use in analysis of NMR data obtained from flexible peptides. J. Comput. Chem., 18: 240–253. doi: 10.1002/(SICI)1096-987X(19970130)18:2<240::AID-JCC8>3.0.CO;2-V
- Issue published online: 7 DEC 1998
- Article first published online: 7 DEC 1998
- Manuscript Accepted: 26 APR 1996
- Manuscript Received: 12 FEB 1996
- Florida State Univ. Supercomputer Comp. Res. Inst. (DOE). Grant Number: DE-FC05-35ER250000
- Doe. Grant Number: DE-FC-05-95ER62070
The Monte Carlo minimization (MCM) method of Li and Scheraga is an efficient tool for generating low energy minimized structures of peptides, in particular the global energy minimum (GEM). In a recent article we proposed an enhancement to MCM, called the free energy Monte Carlo minimization (FMCM) procedure. With FMCM the conformational search is carried out with respect to the harmonic free energy, which approximates the free energy of the potential energy wells around the energy minimized structures (these wells are called localized microstates). In this work we apply both methods to the pentapeptide Leu-enkephalin described by the potential energy function ECEPP, and study their efficiency in identifying the GEM structure as well as the global harmonic free energy (GFM) structure. We also investigate the efficiency of these methods to generate localized microstates, which pertain to different energy and harmonic free energy intervals above the GEM and GFM, respectively. Such microstates constitute an important ingredient of our statistical mechanical methodology for analyzing nuclear magnetic resonance data of flexible peptides. Aspects of this methodology related to the stability properties of the localized microstates are examined. © 1997 by John Wiley & Sons, Inc.