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1995 | 42 | 4 |

Tytuł artykułu

Rapid non-empirical approaches for estimating relative binding free energies

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
Rapid non-empirical methods for estimating binding free energies are reviewed. A novel approach based on the application of the free energy perturbation formula to a biased ensemble is presented. Preliminary results demonstrating the applicability of this approach in protein systems are shown and the potential of this method in structure-based drug design is discussed.

Wydawca

-

Rocznik

Tom

42

Numer

4

Opis fizyczny

p.525-535,fig.

Twórcy

autor
  • Eidgenossische Technische Hochschule, ETH-Zentrum, CH 8092 Switzerland
autor
autor

Bibliografia

  • 1. Kubinyi, H. (1993) QASR: Hansch analysis and related approaches. VCH, Weinheim, Germany.
  • 2. Martin, V.C. (1978) Quantitative drug design: A critical introduction. Marcel Dekker, New York.
  • 3. Kuntz, I.D., Meng, E.C. & Shoichet, B.K. (1994) Structure-based molecular design. Acc. Chem. Res. 27,117-123.
  • 4. Colman, P.M. (1994) Structure-based drug design. Curr. Opin. Struct. Biol. 4, 868-874.
  • 5. van Gunsteren, W.F., King, P.M. & Mark, A.E. (1994) Fundamentals of drug design from a biophysical viewpoint. Quart. Rev. Biophys. 27, 435-481.
  • 6. Mark, A.E. & van Gunsteren, W.F. (1994) De­composition of the free energy of a system in terms specific interactions: Implications for theoretical and experimental studies. /. Mol. Biol. 240,167-176.
  • 7. Beveridge, D.L. & Di Capua, F.M. (1989) Free energy via molecular simulation: Applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18,431^92.
  • 8. Kirkwood, J.G. (1935) Statistical mechanics of fluid mixtures. /. Chem. Phys. 3,300-313.
  • 9. Zwanzig, R.W. (1954) High-temperature equ­ation of state by a perturbation method: I. Non- -polar gases. /. Chem. Phys. 22,1420-1426.
  • 10. Jorgensen, W.L. (1991) Computational insights on intermolecular interactions and binding in solution. Chemtracts: Org. Chem. 4,91-119.
  • 11. van Gunsteren, W.F., Beutler, T.C., Fraternali, F., King, P.M., Mark, A.E. & Smith, P.E. (1993) Computation of free energy in practice: Choice of approximations and accuracy limiting factors; in Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications (van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J., eds.) vol. 2, pp. 315-348, ESCOM Science Publi- shers, Leiden, The Netherlands.
  • 12. Gerber, P.R., Mark, A.E. & van Gunsteren, W.F. (1993) An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. }. Computer- Aided Mole- cular Design 7,305-323.
  • 13. Smith, P.E. & van Gunsteren, W.F. (1994) Pre­dictions of free energy differences from a single simulation of the initial state./. Chem. Phys. 100, 577-585.
  • 14. Levy, R.M., Belhadj, M. & Kitchen, D.B. (1991) Gaussian fluctuation formula for electrostatic free-energy changes. }. Chem. Phys. 95, 3627- -3633.
  • 15. King, G. & Barford, R.A. (1993) Calculation of electrostatic free energy differences with a time-saving approximate method. /. Phys. Chem. 97,8798-8802.
  • 16. Aqvist, J., Medina, C. & Samuelsson, J.-E. (1994) A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7, 385-391.
  • 17. Gilson, M.K. & Honig, B. (1988) Calculation of the total electrostatic energy of a macromo- lecular system: Solvation energies, binding energies, and conformational analysis. Proteins 4,7-18.
  • 18. Sharp, K.A. & Honig, B. (1990) Electrostatic interactions in macromolecules: Theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19,301-332.
  • 19. Sharp, K.A. (1994) Electrostatic interactions in macromolecules. Curr. Opin. Struct. Biol. 4,234- -239.
  • 20. Liu, H., Mark, A.E. & van Gunsteren, W.F. (1995) On estimating the relative free energy of different molecular states with respect to a single reference state. J. Phys. Chem. (in press).
  • 21. Beutler, T.C., Mark, A.E., van Schaik, R.C., Gerber, PR. & van Gunsteren, W.F. (1994) Avoiding singularities and numerical insta­bilities in free energy calculations based on molecular simulation. Chem. Phys. Lett. 222, 529-539.
  • 22. Morton, A., Baase, W.A. & Matthews, B.W. (1995) Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry (in press).
  • 23. Morton, A. «St Matthews, B.W. (1995) Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity. Biochemistry (in press).
  • 24. Berendsen, H.J.C., Postma, J.P.M., van Gun­steren, W.F. & Hermans, J. (1981) Interaction models for water in relation to protein hydration; in Intermolecular Forces (Pullman, B., ed.) pp. 331-342, Reidel, Dordrecht, The Netherlands.25. Berendsen, H.J.C., Postma, J.P.M., van Gun­steren, W.F., DiNola, A. & Haak, J.R. (1984) Molecular dynamics with coupling to an external bath.}. Chem. Phys. 81,3684-3690.
  • 26. Ryckaert, J.-P., Ciccotti, G. & Berendsen, H.J.C. (1977) Numerical integration of the Cartesian equations of motion with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341.
  • 27. van Gunsteren, W.F. & Berendsen, H.J.C. (1987) Groningen Molecular Simulation Library Ma­nual, Biomos, University of Groningen, The Netherlands.
  • 28. Smith, L.J., Mark, A.E., Dobson, C.M. & van Gunsteren, W.F. (1995) Comparison of MD simulations and NMR experiments for hen lysozyme: Analysis of local fluctuations, coope­rative motions, and global changes. Biochemistry 34,10918-10918.
  • 29. Cabani, S., Gianni, P., Mollica, V. & Lepori, L. (1981) Group contributions to the thermody­namic properties of non-ionic organic solutes in dilute aqueous solution. J. Soln. Chem. 10, 563-595.

Typ dokumentu

Bibliografia

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Identyfikator YADDA

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