Download PDF by M. Rami Reddy, Mark D. Erion: Free Energy Calculations in Rational Drug Design

By M. Rami Reddy, Mark D. Erion

ISBN-10: 1441933727

ISBN-13: 9781441933720

Loose strength calculations signify the main actual computational approach on hand for predicting enzyme inhibitor binding affinities. Advances in machine strength within the Nineteen Nineties enabled the sensible program of those calculations in motive drug layout. This booklet represents the 1st accomplished evaluate of this becoming region of study and covers the elemental concept underlying the tactic, a variety of cutting-edge options designed to enhance throughput and dozen examples in which loose power calculations have been used to layout and review strength drug applicants.

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D. A. Pearlman, D. A. Case, J. C. Caldwell, W. S. Ross, T. E. Cheatham III, S. DeBoIt, D. M. Ferguson, G. L. Seibel, and P. A. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comp. Phys. Comm. 91:1 (1995). 61. P. A. Bash, U. C. Singh, R. Langridge, and P. A. Kollman, Free energy calculations by computer simulation, Science 236:564 (1987).

But they make various assumptions or simplifications that allow them to be carried out much more quickly. All of these methods have shown promise on limited data, but as of yet, all are still in the development stage. The linear interaction energy method allows the approximation of the free energy of binding using the relationships64 AG44-= a < &Vvdw> +ft < AVCOB,om^ (34) where the averages are evaluated from a reference state ensemble. This expression is derived from the master equation of FEP assuming linear response theory holds in the regime of interest.

G. Ford, and J. W. Essex, Binding constants of neuraminidase inhibitors: An investigation of the linear interaction energy method, J. Med. Chem. 42:5142 (1999). 68. D. K. Jones-Hertzog and W. K. Jorgensen, Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method, J. Med. Chem. 40:1539 (1997). 69. H. A. Carlson and W. L Jorgensen, An extended linear response method for determining free energies of hydration, J. Phys. Chem. 99:10667 (1995).

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Free Energy Calculations in Rational Drug Design by M. Rami Reddy, Mark D. Erion

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