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Volumn 42, Issue 21, 1999, Pages 4313-4324

Free energy grids: A practical qualitative application of free energy perturbation to ligand design using the OWFEG method

Author keywords

[No Author keywords available]

Indexed keywords

QUINOLINE DERIVATIVE; TACROLIMUS;

EID: 0032698313     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm990133z     Document Type: Article
Times cited : (29)

References (28)
  • 2
    • 0021582448 scopus 로고
    • Ligand-receptor interactions
    • Tembe, B. L.; McCammon, J. A. Ligand-receptor interactions. Comput. Chem. 1984, 8, 281-283.
    • (1984) Comput. Chem. , vol.8 , pp. 281-283
    • Tembe, B.L.1    McCammon, J.A.2
  • 3
    • 0004504539 scopus 로고
    • Monte Carlo simulation of differences in free energies of hydration
    • Jorgensen, W. L.; Ravimohan, C. Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 1985, 83, 3050-3054.
    • (1985) J. Chem. Phys. , vol.83 , pp. 3050-3054
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 4
    • 0000008625 scopus 로고    scopus 로고
    • Free energy calculations: Methods and applications
    • Schleyer, P. V. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F., Schreiner, R. P., Eds.; John Wiley & Sons: New York
    • Pearlman, D. A.; Rao, B. G. Free energy calculations: methods and applications. In Encyclopedia of Computational Chemistry; Schleyer, P. V. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F., Schreiner, R. P., Eds.; John Wiley & Sons: New York, 1998; pp 1036-1061.
    • (1998) Encyclopedia of Computational Chemistry , pp. 1036-1061
    • Pearlman, D.A.1    Rao, B.G.2
  • 5
    • 7044239742 scopus 로고
    • Free energy calculations-applications to chemical and biochemical phenomena
    • Kollman, P. Free energy calculations-applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 6
    • 0029043773 scopus 로고
    • Determination of the differential effects of hydrogen bonding and water release on the binding of FK506 to native and Tyr82 → Phe82 FKBP-12 proteins using free energy simulations
    • Pearlman, D. A.; Connelly, P. R. Determination of the differential effects of hydrogen bonding and water release on the binding of FK506 to native and Tyr82 → Phe82 FKBP-12 proteins using free energy simulations. J. Mol. Biol 1995, 248, 696-717.
    • (1995) J. Mol. Biol , vol.248 , pp. 696-717
    • Pearlman, D.A.1    Connelly, P.R.2
  • 7
    • 0020698476 scopus 로고
    • Dynamics of proteins: Elements and function
    • Karplus, M.; McCammon, J. A. Dynamics of proteins: elements and function. Annu. Rev. Biochem. 1983, 52, 263-300.
    • (1983) Annu. Rev. Biochem. , vol.52 , pp. 263-300
    • Karplus, M.1    McCammon, J.A.2
  • 8
    • 0000812183 scopus 로고
    • Theoretical studies of medium effects on conformational equilibria
    • Jorgensen, W. L. Theoretical studies of medium effects on conformational equilibria. J. Phys. Chem. 1983, 87, 5304-5314.
    • (1983) J. Phys. Chem. , vol.87 , pp. 5304-5314
    • Jorgensen, W.L.1
  • 9
    • 36449005776 scopus 로고
    • The overlooked bond-stretching contribution in free energy perturbation calculations
    • Pearlman, D. A.; Kollman, P. A. The Overlooked Bond-Stretching Contribution in Free Energy Perturbation Calculations. J. Chem. Phys. 1991, 94, 4532-4545.
    • (1991) J. Chem. Phys. , vol.94 , pp. 4532-4545
    • Pearlman, D.A.1    Kollman, P.A.2
  • 10
    • 0000871204 scopus 로고
    • Multiconfiguration thermodynamic integration
    • Straatsma, T. P.; McCammon, J. A. Multiconfiguration Thermodynamic Integration. J. Chem. Phys. 1991, 95, 1175-1188.
    • (1991) J. Chem. Phys. , vol.95 , pp. 1175-1188
    • Straatsma, T.P.1    McCammon, J.A.2
  • 11
    • 84986532462 scopus 로고
    • Free energy difference calculations by thermodynamic integration-difficulties in obtaining a precise value
    • Mitchell, M. J.; McCammon, J. A. Free energy difference calculations by thermodynamic integration-difficulties in obtaining a precise value. J. Comput. Chem. 1991, 12, 271-275.
    • (1991) J. Comput. Chem. , vol.12 , pp. 271-275
    • Mitchell, M.J.1    McCammon, J.A.2
  • 12
    • 84946449187 scopus 로고
    • Convergence of the chemical potential in aqueous simulations
    • Mazor, M.; Pettitt, B. M. Convergence of the chemical potential in aqueous simulations. Mol. Simul. 1991, 6, 1-4.
    • (1991) Mol. Simul. , vol.6 , pp. 1-4
    • Mazor, M.1    Pettitt, B.M.2
  • 13
    • 0344858211 scopus 로고
    • Free energy simulations of methane solvation - A study of integrand convergence properties using thermodynamic integration
    • Fleischman, S. H.; Zichi, D. A. Free energy simulations of methane solvation - a study of integrand convergence properties using thermodynamic integration. J. Chim. Phys. 1991, 88, 2617-2622.
    • (1991) J. Chim. Phys. , vol.88 , pp. 2617-2622
    • Fleischman, S.H.1    Zichi, D.A.2
  • 14
    • 0000441039 scopus 로고
    • Conformational substates and uncertainty in macromolecular free energy calculations
    • Hodel, A.; Simonson, T.; Fox, R. O.; Brunger, A. T. Conformational Substates and Uncertainty in Macromolecular Free Energy Calculations. J. Phys. Chem. 1993, 97, 3409-3417.
    • (1993) J. Phys. Chem. , vol.97 , pp. 3409-3417
    • Hodel, A.1    Simonson, T.2    Fox, R.O.3    Brunger, A.T.4
  • 15
    • 36449004340 scopus 로고
    • Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations
    • Pearlman, D. A. Determining the Contributions of Constraints in Free Energy Calculations: Development, Characterization, and Recommendations. J. Chem. Phys. 1993, 98, 8946-8957.
    • (1993) J. Chem. Phys. , vol.98 , pp. 8946-8957
    • Pearlman, D.A.1
  • 16
    • 84986533552 scopus 로고
    • Free energy derivatives: A new method for probing the convergence problem in free energy calculations
    • Pearlman, D. A. Free Energy Derivatives: A New Method for Probing the Convergence Problem in Free Energy Calculations. J. Comput. Chem. 1994, 15, 105-123.
    • (1994) J. Comput. Chem. , vol.15 , pp. 105-123
    • Pearlman, D.A.1
  • 17
    • 0003241140 scopus 로고    scopus 로고
    • Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy
    • Helms, V.; Wade, R. C. Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. J. Comput. Chem. 1997, 18, 449-462.
    • (1997) J. Comput. Chem. , vol.18 , pp. 449-462
    • Helms, V.1    Wade, R.C.2
  • 18
    • 0024377366 scopus 로고
    • Selective elimination of interactions: A method for assessing thermodynamic contributions to ligand binding with application to rhinovirus antivirals
    • Lau, W. F.; Pettitt, B. M, Selective Elimination of Interactions: A Method for Assessing Thermodynamic Contributions to Ligand Binding with Application to Rhinovirus Antivirals. J. Med. Chem. 1989, 32, 2542-2547.
    • (1989) J. Med. Chem. , vol.32 , pp. 2542-2547
    • Lau, W.F.1    Pettitt, B.M.2
  • 19
    • 0032058875 scopus 로고    scopus 로고
    • The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors
    • Radmer, R. J.; Kollman, P. A. The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors. J. Comput.-Aided Mol. Des. 1998, 12, 215-227.
    • (1998) J. Comput.-aided Mol. Des. , vol.12 , pp. 215-227
    • Radmer, R.J.1    Kollman, P.A.2
  • 20
    • 0026030568 scopus 로고
    • Chemistry and biology of the immunophilins and their immunosuppressive ligands
    • Schreiber, S. L. Chemistry and biology of the immunophilins and their immunosuppressive ligands. Science 1991, 251, 283-287.
    • (1991) Science , vol.251 , pp. 283-287
    • Schreiber, S.L.1
  • 22
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An All Atom Force Field for Simulations of Proteins and Nucleic Acids. J. Comput. Chem. 1986, 7, 230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 23
    • 0345393437 scopus 로고    scopus 로고
    • Quanta97; Molecular Simulations Incorporated: San Diego, CA, 1997
    • Quanta97; Molecular Simulations Incorporated: San Diego, CA, 1997.
  • 25
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-Alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes. J. Comput. Phys. 1977, 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 27
    • 0002611483 scopus 로고
    • Estimation of statistical errors in molecular simulation calculations
    • Straatsma, T. P.; Berendsen, H. J. C.; Stam, A. J. Estimation of Statistical Errors in Molecular Simulation Calculations. Mol. Phys. 1986, 57, 89-95.
    • (1986) Mol. Phys. , vol.57 , pp. 89-95
    • Straatsma, T.P.1    Berendsen, H.J.C.2    Stam, A.J.3
  • 28
    • 0002485251 scopus 로고
    • How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches
    • Pearlman, D. A. How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches. J. Biomol. NMR 1994, 4, 1-16.
    • (1994) J. Biomol. NMR , vol.4 , pp. 1-16
    • Pearlman, D.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.