메뉴 건너뛰기




Volumn 2, Issue 2, 2009, Pages 148-153

Quantum mechanical calculations for binding sites of metalloproteins

Author keywords

Binding site; DFT; Docking; Metalloprotein; QM MM

Indexed keywords


EID: 70449091473     PISSN: 19760280     EISSN: 20927843     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (2)

References (30)
  • 1
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin, I., Ma, B.Y., Wolfson, H. & Nussinov, R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins-Structure Function and Genetics 47, 409-443 (2002).
    • (2002) Proteins-Structure Function and Genetics , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.Y.2    Wolfson, H.3    Nussinov, R.4
  • 3
    • 0035416126 scopus 로고    scopus 로고
    • High-throughput docking for lead generation
    • Abagyan, R. & Totrov, M. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5, 375-382 (2001).
    • (2001) Curr. Opin. Chem. Biol , vol.5 , pp. 375-382
    • Abagyan, R.1    Totrov, M.2
  • 4
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I.D. Structure-based strategies for drug design and discovery. Science 257, 1078-1082 (1992).
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 5
    • 0034677966 scopus 로고    scopus 로고
    • Drug discovery: A historical perspective
    • Drews, J. Drug discovery: A historical perspective. Science 287, 1960-1964 (2000).
    • (2000) Science , vol.287 , pp. 1960-1964
    • Drews, J.1
  • 7
    • 11144313018 scopus 로고    scopus 로고
    • The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals
    • Cho, A.E. et al. The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals. J. Comput. Chem. 26, 48-71 (2005).
    • (2005) J. Comput. Chem , vol.26 , pp. 48-71
    • Cho, A.E.1
  • 8
    • 0033388757 scopus 로고    scopus 로고
    • Ligand docking and screening with FlexX. Med
    • Kramer, B., Metz, G., Rarey, M. & Lengauer, T. Ligand docking and screening with FlexX. Med. Chem. Res. 9, 463-478 (1999).
    • (1999) Chem. Res , vol.9 , pp. 463-478
    • Kramer, B.1    Metz, G.2    Rarey, M.3    Lengauer, T.4
  • 10
    • 20344403522 scopus 로고    scopus 로고
    • Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/ MM) approach
    • Cho, A.E., Guallar, V., Berne, B.J. & Friesner, R. Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/ MM) approach. J. Comput. Chem. 26, 915-931 (2005).
    • (2005) J. Comput. Chem , vol.26 , pp. 915-931
    • Cho, A.E.1    Guallar, V.2    Berne, B.J.3    Friesner, R.4
  • 11
    • 56649118415 scopus 로고    scopus 로고
    • Effect of quantum mechanical charges in binding sites of metalloproteins
    • Cho, A.E. Effect of quantum mechanical charges in binding sites of metalloproteins. BioChip J. 1, 70-75 (2007).
    • (2007) BioChip J , vol.1 , pp. 70-75
    • Cho, A.E.1
  • 12
    • 7744244599 scopus 로고    scopus 로고
    • Recent advances in zinc enzymology
    • Lipscomb, W.N. & Strater, N. Recent advances in zinc enzymology. Chem. Rev. 96, 2375-2433 (1996).
    • (1996) Chem. Rev , vol.96 , pp. 2375-2433
    • Lipscomb, W.N.1    Strater, N.2
  • 13
    • 0035811217 scopus 로고    scopus 로고
    • Models for protein-zinc ion binding sites. II. The catalytic sites
    • Deerfield, D.W., Carter, C.W. & Pedersen, L.G. Models for protein-zinc ion binding sites. II. The catalytic sites. Int. J. Quantum Chem. 83, 150-165 (2001).
    • (2001) Int. J. Quantum Chem , vol.83 , pp. 150-165
    • Deerfield, D.W.1    Carter, C.W.2    Pedersen, L.G.3
  • 14
    • 0033743281 scopus 로고    scopus 로고
    • Metal binding in proteins: The effect of the dielectric medium
    • Dudev, T. & Lim, C. Metal binding in proteins: The effect of the dielectric medium. J. Phys. Chem. B 104, 3692-3694 (2000).
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3692-3694
    • Dudev, T.1    Lim, C.2
  • 16
    • 0041654899 scopus 로고    scopus 로고
    • Docking studies of matrix metalloproteinase inhibitors: Zinc parameter optimization to improve the binding free energy prediction
    • Hu, X. & Shelver, W.H. Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction. J. Mol. Graph. 22, 115-126 (2003).
    • (2003) J. Mol. Graph , vol.22 , pp. 115-126
    • Hu, X.1    Shelver, W.H.2
  • 17
    • 23944459025 scopus 로고    scopus 로고
    • A combination of docking, QM /MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
    • Khandelwal, A. et al. A combination of docking, QM /MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J. Med. Chem. 48, 5437-5447 (2005).
    • (2005) J. Med. Chem , vol.48 , pp. 5437-5447
    • Khandelwal, A.1
  • 18
    • 13344275187 scopus 로고    scopus 로고
    • Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase
    • Strynadka, N.C.J. et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat. Struct. Mol. Biol. 3, 233-239 (1996).
    • (1996) Nat. Struct. Mol. Biol , vol.3 , pp. 233-239
    • Strynadka, N.C.J.1
  • 19
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • Friesner, R.A. et al. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47, 1739-1749 (2004).
    • (2004) J. Med. Chem , vol.47 , pp. 1739-1749
    • Friesner, R.A.1
  • 20
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M.D., Murray, C.W., Auton, T.R., Paolini, G.V. & Mee, R.P. Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 11, 425-445 (1997).
    • (1997) J. Comput. Aided Mol. Des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 21
    • 20344403522 scopus 로고    scopus 로고
    • Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical(QM/MM) approach
    • Cho, A.E., Guallar, V., Berne, B.J. & Friesner, R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical(QM/MM) approach. J. Comput. Chem. 26, 915-31 (2005).
    • (2005) J. Comput. Chem , vol.26 , pp. 915-931
    • Cho, A.E.1    Guallar, V.2    Berne, B.J.3    Friesner, R.4
  • 22
    • 0011644592 scopus 로고    scopus 로고
    • Thoughts about density functional theory in 1998
    • Kohn, W. Thoughts about density functional theory in 1998. J. Comput. Chem. 20, 1-1 (1999).
    • (1999) J. Comput. Chem , vol.20 , pp. 1-1
    • Kohn, W.1
  • 25
    • 70349963254 scopus 로고    scopus 로고
    • Diffuse functions in the 6-31G basis set for atoms K through Zn
    • Tran, J.M., Rassolov, V.A., Ratner, M.A. & Pople, J.A. Diffuse functions in the 6-31G basis set for atoms K through Zn. J. Am. Chem. Soc. 217, U443-U443 (1999).
    • (1999) J. Am. Chem. Soc , vol.217
    • Tran, J.M.1    Rassolov, V.A.2    Ratner, M.A.3    Pople, J.A.4
  • 26
    • 34250817103 scopus 로고
    • A new mixing of hartree-fock and local density-functional theories
    • Becke, A.D. A new mixing of hartree-fock and local density-functional theories. J. Chem. Phys. 98, 1372-1377 (1993).
    • (1993) J. Chem. Phys , vol.98 , pp. 1372-1377
    • Becke, A.D.1
  • 27
    • 33645716728 scopus 로고
    • Comparison of density-functional and Mp2 calculations on the water monomer and dimer
    • Kim, K. & Jordan, K.D. Comparison of density-functional and Mp2 calculations on the water monomer and dimer. J. Phys. Chem. A 98, 10089-10094 (1994).
    • (1994) J. Phys. Chem. A , vol.98 , pp. 10089-10094
    • Kim, K.1    Jordan, K.D.2
  • 28
    • 0001322105 scopus 로고    scopus 로고
    • Rationale for mixing exact exchange with density functional approximations
    • Perdew, J.P., Emzerhof, M. & Burke, K. Rationale for mixing exact exchange with density functional approximations. J. Chem. Phys. 105, 9982-9985 (1996).
    • (1996) J. Chem. Phys , vol.105 , pp. 9982-9985
    • Perdew, J.P.1    Emzerhof, M.2    Burke, K.3
  • 29
    • 33751157732 scopus 로고
    • Ab-initio calculation of vibrational absorption and circular-dichroism spectra using density-functional force-fields
    • Stephens, P.J., Devlin, F.J., Chabalowski, C.F. & Frisch, M.J. Ab-initio calculation of vibrational absorption and circular-dichroism spectra using density- functional force-fields. J. Phys. Chem. A 98, 11623-11627 (1994).
    • (1994) J. Phys. Chem. A , vol.98 , pp. 11623-11627
    • Stephens, P.J.1    Devlin, F.J.2    Chabalowski, C.F.3    Frisch, M.J.4
  • 30
    • 0001420061 scopus 로고    scopus 로고
    • Mixed ab initio QM/ MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
    • Philipp, D.M. & Friesner, R.A. Mixed ab initio QM/ MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. J. Comput. Chem. 20, 1468-1494 (1999).
    • (1999) J. Comput. Chem , vol.20 , pp. 1468-1494
    • Philipp, D.M.1    Friesner, R.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.