Targeted free energy perturbation

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 65, Issue 4, 2002, Pages

  Jarzynski, C ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; DRUG PRODUCTS; PERTURBATION TECHNIQUES; PHASE TRANSITIONS; PRODUCT DESIGN; STATISTICAL MECHANICS; TEMPERATURE DISTRIBUTION;

ENERGY FUNCTIONS; FREE ENERGY PERTURBATIONS (FEP); INTERNAL ENERGY; SPATIAL TRANSLATION;

FREE ENERGY;

EID: 41349105094     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.65.046122     Document Type: Article

References (24)

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2. See, e.g., D. Chandler, Introduction to Modern Statistical Mechanics (Oxford University Press, New York, 1987); D. Frenkel and B. Smit, Understanding Molecular Simulation; From Algorithms to Applications (Academic Press, San Diego, 1996).
3. Free Energy Calculations in Rational Drug Design, edited by M.R. Reddy and M.D. Erion (Kluwer, Dordrecht, 2001).
4. G.J. Ackland (unpublished).
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18. The problem of estimating Δ F between alchemically different molecules or molecular complexes is a central problem of rational drug design; see Ref. [2].
19. Extensive research along these lines has been carried out for protein molecules; see, e.g., the review by A. Kitao and N. Go, Curr. Opin. Struct. Biol. 9, 164 (1999).
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21. See, for instance, K. Lum, D. Chandler, and J.D. Weeks, J. Phys. Chem. B 103, 4570 (1999); O. Hummer, S. Garde, A.E. Garcia, and L.R. Pratt, Chem. Phys. 258, 349 (2000), and related references.
22. For complicated cavity geometries, analogous mappings could be constructed numerically at relatively low cost.
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24. X.-L. Meng and S. Schilling, J. Computat. Graph Statis, (to be published).