A free energy based Monte Carlo minimization procedure for biomolecules
Journal Article
·
· Journal of Physical Chemistry; (United States)
- Protein Design Lab., Inc., Mountain View, CA (United States)
- Florida State Univ., Tallahassee, FL (United States)
The Monte Carlo minimization (MCM) method of Li and Scheraga (Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611) is a highly efficient procedure for generating low-energy structures of macromolecules and therefore has been used extensively. We propose to enhance this method by carrying out the conformational search with respect to the harmonic free energy rather than the energy. This free energy based MCM (FMCM) procedure has been applied initially to the pentapeptide met-enkephalin, modeled by the potential energy function ECEPP. The results demonstrate that FMCM is effective with a negligible extra computational cost and therefore has the potential to become an important computational tool. Thus, within a range of 1 kcal/mol above the global harmonic free energy minimum, structures were generated with energy of up to 8.3 kcal/mol above the global energy minimum (GEM). Also, three conformations were identified with lower free energy than that of the GEM structure. Some of these structures are very unlikely to be detected by the usual MCM method. 27 refs., 1 tab.
- OSTI ID:
- 6904269
- Journal Information:
- Journal of Physical Chemistry; (United States), Journal Name: Journal of Physical Chemistry; (United States) Vol. 98:38; ISSN JPCHAX; ISSN 0022-3654
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400201 -- Chemical & Physicochemical Properties
550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
661300 -- Other Aspects of Physical Science-- (1992-)
71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
99 GENERAL AND MISCELLANEOUS
990200 -- Mathematics & Computers
CALCULATION METHODS
COMPILED DATA
DATA
ENERGY
FREE ENERGY
INFORMATION
MATHEMATICAL MODELS
MOLECULAR STRUCTURE
MONTE CARLO METHOD
NUMERICAL DATA
ORGANIC COMPOUNDS
PEPTIDES
PHYSICAL PROPERTIES
POLYPEPTIDES
PROBABILITY
PROTEINS
THERMODYNAMIC PROPERTIES
400201 -- Chemical & Physicochemical Properties
550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
661300 -- Other Aspects of Physical Science-- (1992-)
71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
99 GENERAL AND MISCELLANEOUS
990200 -- Mathematics & Computers
CALCULATION METHODS
COMPILED DATA
DATA
ENERGY
FREE ENERGY
INFORMATION
MATHEMATICAL MODELS
MOLECULAR STRUCTURE
MONTE CARLO METHOD
NUMERICAL DATA
ORGANIC COMPOUNDS
PEPTIDES
PHYSICAL PROPERTIES
POLYPEPTIDES
PROBABILITY
PROTEINS
THERMODYNAMIC PROPERTIES