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Volumn 7, Issue 10, 2007, Pages 1030-1038

Structure based drug design for HIV protease: From molecular modeling to cheminformatics

Author keywords

Darunavir; Docking; Drug resistant HIV; Molecular mechanics; Self organizing map; SMILES notation

Indexed keywords

AMPRENAVIR; DARUNAVIR; DNA; DOCKING PROTEIN; GENOMIC DNA; INDINAVIR; LIGAND; MOZENAVIR; NELFINAVIR; PROTEIN KINASE INHIBITOR; PROTEINASE; PROTEINASE INHIBITOR; SAQUINAVIR; SIALIDASE INHIBITOR; TIPRANAVIR;

EID: 34447270269     PISSN: 15680266     EISSN: None     Source Type: Journal    
DOI: 10.2174/156802607780906744     Document Type: Review
Times cited : (12)

References (100)
  • 1
    • 1642323740 scopus 로고    scopus 로고
    • Protein kinase inhibitors: Insights into drug design from structure
    • Noble, M. E.; Endicott; J. A.; Johnson, L. N. Protein kinase inhibitors: insights into drug design from structure, Science 2004, 303, 1800-1805.
    • (2004) Science , vol.303 , pp. 1800-1805
    • Noble, M.E.1    Endicott, J.A.2    Johnson, L.N.3
  • 3
    • 0031804609 scopus 로고    scopus 로고
    • Inhibitors of HIV-1 protease: A major success of structure-assisted drug design
    • Wlodawer, A.; Vondrasek, J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 249-284.
    • (1998) Annu. Rev. Biophys. Biomol. Struct , vol.27 , pp. 249-284
    • Wlodawer, A.1    Vondrasek, J.2
  • 5
    • 0036222716 scopus 로고    scopus 로고
    • Genotypic testing for human immunodeficiency virus type 1 drug resistance
    • Shafer, R. W. Genotypic testing for human immunodeficiency virus type 1 drug resistance. Clin. Microbiol. Rev. 2002, 15, 247-277.
    • (2002) Clin. Microbiol. Rev , vol.15 , pp. 247-277
    • Shafer, R.W.1
  • 6
    • 34447257838 scopus 로고    scopus 로고
    • Potential-Based Simulation and Molecular Modeling
    • Rieth, M, Schommers, W, Eds, American Scientific Publishers: Forschungszentrum Karlsruhe, Germany
    • Volarath, P.; Harrison, R. W. Potential-Based Simulation and Molecular Modeling. In Handbook of Theoretical and Computational Nanotechnology; Rieth, M.; Schommers, W.; Eds.; American Scientific Publishers: Forschungszentrum Karlsruhe, Germany, 2006; pp 547-587.
    • (2006) Handbook of Theoretical and Computational Nanotechnology , pp. 547-587
    • Volarath, P.1    Harrison, R.W.2
  • 7
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov. 2004, 3, 935-949.
    • (2004) Nat. Rev. Drug Discov , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 8
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004, 56, 235-249.
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 9
    • 23844477186 scopus 로고    scopus 로고
    • Application of 3D-QSAR techniques in anti-HIV-1 drug design-an overview
    • Debnath, A. K. Application of 3D-QSAR techniques in anti-HIV-1 drug design-an overview. Curr. Pharm. Des. 2005, 11, 3091-3110.
    • (2005) Curr. Pharm. Des , vol.11 , pp. 3091-3110
    • Debnath, A.K.1
  • 10
    • 0041922335 scopus 로고    scopus 로고
    • HIV-1 protease inhibitors: A comparative QSAR analysis
    • Kurup, A.; Mekapati, S. B.; Garg, R.; Hansch, C. HIV-1 protease inhibitors: a comparative QSAR analysis. Curr. Med. Chem. 2003, 10, 1679-1688.
    • (2003) Curr. Med. Chem , vol.10 , pp. 1679-1688
    • Kurup, A.1    Mekapati, S.B.2    Garg, R.3    Hansch, C.4
  • 11
    • 19644377421 scopus 로고    scopus 로고
    • Prediction methods and databases within chemoinformatics: Emphasis on drugs and drug candidates
    • Jonsdottir, S. O.; Jorgensen, F. S.; Brunak, S. Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics 2005, 21, 2145-2160.
    • (2005) Bioinformatics , vol.21 , pp. 2145-2160
    • Jonsdottir, S.O.1    Jorgensen, F.S.2    Brunak, S.3
  • 12
    • 2942534993 scopus 로고    scopus 로고
    • HIV protease inhibition: Limited recent progress and advances in understanding current pitfalls
    • Rodriguez-Barrios, F.; Gago, F. HIV protease inhibition: limited recent progress and advances in understanding current pitfalls. Curr. Top. Med. Chem. 2004, 4, 991-1007.
    • (2004) Curr. Top. Med. Chem , vol.4 , pp. 991-1007
    • Rodriguez-Barrios, F.1    Gago, F.2
  • 15
    • 11144354478 scopus 로고    scopus 로고
    • High Resolution Crystal Structures of HIV-1 Protease with a Potent Non-peptide Inhibitor (UIC-94017) Active against Multi-Drug Resistant Clinical Strains
    • Tie, Y.; Boross, P. I.; Wang, Y.-F.; Gaddis, L.; Hussain, A. K.; Leshchenko, S.; Ghosh, A. K.; Louis, J. M.; Harrison, R. W.; Weber, I. T. High Resolution Crystal Structures of HIV-1 Protease with a Potent Non-peptide Inhibitor (UIC-94017) Active against Multi-Drug Resistant Clinical Strains. J. Mol. Biol. 2004, 338, 341-352.
    • (2004) J. Mol. Biol , vol.338 , pp. 341-352
    • Tie, Y.1    Boross, P.I.2    Wang, Y.-F.3    Gaddis, L.4    Hussain, A.K.5    Leshchenko, S.6    Ghosh, A.K.7    Louis, J.M.8    Harrison, R.W.9    Weber, I.T.10
  • 18
    • 4444351490 scopus 로고    scopus 로고
    • Empirical Force Fields for Biological Macromolecules: Overview and Issues
    • MacKerell, A. D., Jr. Empirical Force Fields for Biological Macromolecules: Overview and Issues. J. Comp. Chem. 2004, 25, 1584-1604.
    • (2004) J. Comp. Chem , vol.25 , pp. 1584-1604
    • MacKerell Jr., A.D.1
  • 19
    • 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. Comp. Chem. 1986, 7, 230-252.
    • (1986) J. Comp. Chem , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 20
    • 0042041206 scopus 로고
    • UFF a full periodic table force field for molecular mechanics and molecular dynamics simulations
    • Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A. I.; Skiff, W. M. UFF a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024-10035.
    • (1992) J. Am. Chem. Soc , vol.114 , pp. 10024-10035
    • Rappe, A.K.1    Casewit, C.J.2    Colwell, K.S.3    Goddard, W.A.I.4    Skiff, W.M.5
  • 21
    • 0024821263 scopus 로고
    • Molecular mechanics: The MM3 force field for hydrocarbons
    • Allinger, N. L.; Yuh, Y. H.; Lii, J. H. Molecular mechanics: The MM3 force field for hydrocarbons. J. Am. Chem. Soc. 1989, 111, 8551-8565.
    • (1989) J. Am. Chem. Soc , vol.111 , pp. 8551-8565
    • Allinger, N.L.1    Yuh, Y.H.2    Lii, J.H.3
  • 23
    • 0029790550 scopus 로고    scopus 로고
    • Molecular Mechanics Calculations on HIV-1 Protease with Peptide Substrates Correlate with Experimental Data
    • Weber, I. T.; Harrison, R. W. Molecular Mechanics Calculations on HIV-1 Protease with Peptide Substrates Correlate with Experimental Data. Protein Eng. 1996, 9, 679-690.
    • (1996) Protein Eng , vol.9 , pp. 679-690
    • Weber, I.T.1    Harrison, R.W.2
  • 24
    • 0030685159 scopus 로고    scopus 로고
    • Molecular Mechanics Calculations on Rous sarcoma virus Protease with Peptide Substrates
    • Weber, I. T.; Harrison, R. W. Molecular Mechanics Calculations on Rous sarcoma virus Protease with Peptide Substrates. Prot. Sci. 1997, 6, 2365-2374.
    • (1997) Prot. Sci , vol.6 , pp. 2365-2374
    • Weber, I.T.1    Harrison, R.W.2
  • 25
    • 0008878905 scopus 로고    scopus 로고
    • Weber, I. T.; Harrison, R. W. Molecular Mechanics Calculations on Protein-Ligand Complexes. In 3D QSAR in Drug Design. 2. Ligand-Protein Interactions and Molecular Similarity.; Kubinyi, H.; Folkers, G.; Martin, Y.; Eds.; Kluwer Academic Publishers: Dordrecht, the Netherlands, 1998; pp. 115-127.
    • Weber, I. T.; Harrison, R. W. Molecular Mechanics Calculations on Protein-Ligand Complexes. In 3D QSAR in Drug Design. Vol. 2. Ligand-Protein Interactions and Molecular Similarity.; Kubinyi, H.; Folkers, G.; Martin, Y.; Eds.; Kluwer Academic Publishers: Dordrecht, the Netherlands, 1998; pp. 115-127.
  • 26
    • 0028519286 scopus 로고
    • Prediction of Novel Serine Protease Inhibitors
    • Harrison, R. W.; Kurinov, I. V. Prediction of Novel Serine Protease Inhibitors. Nat. Struct. Biol. 1994, 1, 735-743.
    • (1994) Nat. Struct. Biol , vol.1 , pp. 735-743
    • Harrison, R.W.1    Kurinov, I.V.2
  • 27
    • 0029030222 scopus 로고
    • Probing structure-function relationships in humar immunodeficiency virus type 1 protesse via molecular dynamics simulation
    • Harte, W. E. J.; Beveridge, D. L. Probing structure-function relationships in humar immunodeficiency virus type 1 protesse via molecular dynamics simulation. Methods Enzymol. 1994, 241, 178-195.
    • (1994) Methods Enzymol , vol.241 , pp. 178-195
    • Harte, W.E.J.1    Beveridge, D.L.2
  • 28
    • 0028173594 scopus 로고
    • Molecular dynamics simulations of HIV-1 protease with peptide substrate
    • Harrison, R. W.; Weber, I. T. Molecular dynamics simulations of HIV-1 protease with peptide substrate. Protein Eng. 1994, 7, 1353-1363.
    • (1994) Protein Eng , vol.7 , pp. 1353-1363
    • Harrison, R.W.1    Weber, I.T.2
  • 29
    • 0031049559 scopus 로고    scopus 로고
    • Analysis of the structure of HIV-1 protesse complexed with a hexapeptide inhibitor, part II: Molecular dynamic studies of the active site region
    • Geller, M.; Miller, M.; Swanson, S. M.; Maizel, J. Analysis of the structure of HIV-1 protesse complexed with a hexapeptide inhibitor, part II: molecular dynamic studies of the active site region. Proteins 1997, 27, 195-203.
    • (1997) Proteins , vol.27 , pp. 195-203
    • Geller, M.1    Miller, M.2    Swanson, S.M.3    Maizel, J.4
  • 30
    • 0030598997 scopus 로고    scopus 로고
    • A combined quantum/ classical molecular dynamics study of the catalytic mechanism of HIV protease
    • Liu, H.; Müller-Plathe, F.; Van Gusteren, W. F. A combined quantum/ classical molecular dynamics study of the catalytic mechanism of HIV protease. J. Mol. Biol. 1996, 261, 454-469.
    • (1996) J. Mol. Biol , vol.261 , pp. 454-469
    • Liu, H.1    Müller-Plathe, F.2    Van Gusteren, W.F.3
  • 31
    • 0035850539 scopus 로고    scopus 로고
    • Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site
    • Piana, S.; Sebastiani, D.; Carloni, P.; Parrinello, M. Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. J. Am. Chem. Soc. 2001, 123, 8730-8737.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 8730-8737
    • Piana, S.1    Sebastiani, D.2    Carloni, P.3    Parrinello, M.4
  • 32
    • 0035997007 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease
    • Trylska, J.; Bala, P.; Geller, M.; Grochowski, P. Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease. Biophys. J. 2002, 83, 794-807.
    • (2002) Biophys. J , vol.83 , pp. 794-807
    • Trylska, J.1    Bala, P.2    Geller, M.3    Grochowski, P.4
  • 33
    • 0029863567 scopus 로고    scopus 로고
    • Inhibition and catalytic mechanism of HIV-1 aspartic protease
    • Silva, A. M.; Cachau, R. E.; Sham, H. L.; Erickson, J. W. Inhibition and catalytic mechanism of HIV-1 aspartic protease. J. Mol. Biol. 1996, 255, 321-346.
    • (1996) J. Mol. Biol , vol.255 , pp. 321-346
    • Silva, A.M.1    Cachau, R.E.2    Sham, H.L.3    Erickson, J.W.4
  • 34
    • 1642452881 scopus 로고    scopus 로고
    • The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease
    • Trylska, J.; Grochowski, P.; McCammon, J. A. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease. Protein Sci. 2004, 13, 513-528.
    • (2004) Protein Sci , vol.13 , pp. 513-528
    • Trylska, J.1    Grochowski, P.2    McCammon, J.A.3
  • 35
    • 0029063951 scopus 로고    scopus 로고
    • Holloway, M. K.; Wai, J. M.; Halgren, T. A.; Fitzgerald, P. M.; Vacca, J. P.; Dorsey, B. D.; Levin, R. B.; Thompson, W. J.; Chen, L. J.; deSolms, S. J.; Gaffin, N.; Ghosh, A. K.; Giuliani, E. A.; Graham, S. L.; Guare, J. P.; Hungate, R. W.; Lyle, T. A.; Sanders, W. M.; Tucker, T. J.; Wiggins, M.; Wiscount, C. M.; Woltersdorf, O. W.; Young, S. D.; Darke, P. L.; Zugay, J. A. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 1995, 38, 305-317.
    • Holloway, M. K.; Wai, J. M.; Halgren, T. A.; Fitzgerald, P. M.; Vacca, J. P.; Dorsey, B. D.; Levin, R. B.; Thompson, W. J.; Chen, L. J.; deSolms, S. J.; Gaffin, N.; Ghosh, A. K.; Giuliani, E. A.; Graham, S. L.; Guare, J. P.; Hungate, R. W.; Lyle, T. A.; Sanders, W. M.; Tucker, T. J.; Wiggins, M.; Wiscount, C. M.; Woltersdorf, O. W.; Young, S. D.; Darke, P. L.; Zugay, J. A. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 1995, 38, 305-317.
  • 36
    • 0030078277 scopus 로고    scopus 로고
    • Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods
    • Rao, B. G.; Kim, E. E.; Murcko, M. A. Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods. J. Comput. Aided Mol. Des. 1996, 10, 23-30.
    • (1996) J. Comput. Aided Mol. Des , vol.10 , pp. 23-30
    • Rao, B.G.1    Kim, E.E.2    Murcko, M.A.3
  • 37
    • 0028958868 scopus 로고
    • Flap opening in HIV-1 protease simulated by "activated" molecular dynamics
    • Collins, J. R.; Burt, S. K.; Erickson, J. W. Flap opening in HIV-1 protease simulated by "activated" molecular dynamics. Nat. Struct. Biol. 1995, 2, 334-338.
    • (1995) Nat. Struct. Biol , vol.2 , pp. 334-338
    • Collins, J.R.1    Burt, S.K.2    Erickson, J.W.3
  • 38
    • 0034483901 scopus 로고    scopus 로고
    • Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
    • Scott, W. R.; Schiffer, C. A. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 2000, 8, 1259-1265.
    • (2000) Structure , vol.8 , pp. 1259-1265
    • Scott, W.R.1    Schiffer, C.A.2
  • 39
    • 0037963159 scopus 로고    scopus 로고
    • Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations
    • Kurt, N.; Scott, W. R.; Schiffer, C. A.; Haliloglu, T. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins 2003, 51, 409-422.
    • (2003) Proteins , vol.51 , pp. 409-422
    • Kurt, N.1    Scott, W.R.2    Schiffer, C.A.3    Haliloglu, T.4
  • 40
    • 1842454635 scopus 로고    scopus 로고
    • HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs
    • Perryman, A. L.; Lin, J. H.; McCammon, J. A. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci. 2004, 13, 1108-1123.
    • (2004) Protein Sci , vol.13 , pp. 1108-1123
    • Perryman, A.L.1    Lin, J.H.2    McCammon, J.A.3
  • 41
    • 4544323776 scopus 로고    scopus 로고
    • Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations
    • Lepsik, M.; Kriz, Z.; Havlas, Z. Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations. Proteins 2004, 57, 279-293.
    • (2004) Proteins , vol.57 , pp. 279-293
    • Lepsik, M.1    Kriz, Z.2    Havlas, Z.3
  • 42
    • 84962343778 scopus 로고    scopus 로고
    • Nivesanond, K.; Peeters, A.; Lamoen, D.; van Alsenoy, C. Ab Initio Calculation of the Interaction Energy in the P2 Binding Pocket of HIV-1 Protease. Int. J. Quant. Chem. 2005, 105, 292-299.
    • Nivesanond, K.; Peeters, A.; Lamoen, D.; van Alsenoy, C. Ab Initio Calculation of the Interaction Energy in the P2 Binding Pocket of HIV-1 Protease. Int. J. Quant. Chem. 2005, 105, 292-299.
  • 43
    • 11144235131 scopus 로고    scopus 로고
    • A combined QM/MM approach to protein-ligand interactions: Polarization effects of the HIV-1 protease on selected high affinity inhibitors
    • Hensen, C.; Hermann, J. C.; Nam, K.; Ma, S.; Gao, J.; Holtje, H. D. A combined QM/MM approach to protein-ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors. J. Med. Chem. 2004, 47, 6673-6680.
    • (2004) J. Med. Chem , vol.47 , pp. 6673-6680
    • Hensen, C.1    Hermann, J.C.2    Nam, K.3    Ma, S.4    Gao, J.5    Holtje, H.D.6
  • 44
    • 4544226381 scopus 로고    scopus 로고
    • Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method
    • Parish, C. A.; Yarger, M.; Sinclair, K.; Dure, M.; Goldberg, A. Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method. J. Med. Chem. 2004, 47, 4838-4850.
    • (2004) J. Med. Chem , vol.47 , pp. 4838-4850
    • Parish, C.A.1    Yarger, M.2    Sinclair, K.3    Dure, M.4    Goldberg, A.5
  • 45
    • 0033001019 scopus 로고    scopus 로고
    • Molecular Mechanics Analysis of Drug Resistant Mutants of HIV Protease
    • Weber, I. T.; Harrison, R. W. Molecular Mechanics Analysis of Drug Resistant Mutants of HIV Protease. Protein Eng. 1999, 12, 469-474.
    • (1999) Protein Eng , vol.12 , pp. 469-474
    • Weber, I.T.1    Harrison, R.W.2
  • 46
    • 0041341885 scopus 로고    scopus 로고
    • Structure-based phenotyping predicts HIV-1 protease inhibitor resistance
    • Shenderovich, M. D.; Kagan, R. M.; Heseltine, P. N.; Ramnarayan, K. Structure-based phenotyping predicts HIV-1 protease inhibitor resistance. Protein Sci. 2003, 12, 1706-1718.
    • (2003) Protein Sci , vol.12 , pp. 1706-1718
    • Shenderovich, M.D.1    Kagan, R.M.2    Heseltine, P.N.3    Ramnarayan, K.4
  • 47
    • 0032469463 scopus 로고    scopus 로고
    • Molecular mechanisms of resistance: Free energy calculations of mutation effects on inhibitor binding to HIV-1 protease
    • Rick, S. W.; Topol, I. A.; Erickson, J. W.; Burt, S. K. Molecular mechanisms of resistance: free energy calculations of mutation effects on inhibitor binding to HIV-1 protease. Protein Sci. 1998, 7, 1750-1756.
    • (1998) Protein Sci , vol.7 , pp. 1750-1756
    • Rick, S.W.1    Topol, I.A.2    Erickson, J.W.3    Burt, S.K.4
  • 48
    • 10944234802 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of 14 HIV Protease Mutants in Complexes with Indinavir
    • Chen, X.; Weber, I. T.; Harrison, R. W. Molecular Dynamics Simulations of 14 HIV Protease Mutants in Complexes with Indinavir. J. Mol. Model. 2004, 10, 373-381.
    • (2004) J. Mol. Model , vol.10 , pp. 373-381
    • Chen, X.1    Weber, I.T.2    Harrison, R.W.3
  • 49
    • 0036786493 scopus 로고    scopus 로고
    • Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations
    • Piana, S.; Carloni, P.; Rothlisberger, U. Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci. 2002, 11, 2393-2402.
    • (2002) Protein Sci , vol.11 , pp. 2393-2402
    • Piana, S.1    Carloni, P.2    Rothlisberger, U.3
  • 50
    • 0035910029 scopus 로고    scopus 로고
    • Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
    • Wang, W.; Kollman, P. A. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc. Natl. Acad. Sci. USA 2001, 98, 14937-14942.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 14937-14942
    • Wang, W.1    Kollman, P.A.2
  • 51
    • 0031717170 scopus 로고    scopus 로고
    • Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
    • Schaffer, L.; Verkhivker, G. M. Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins 1998, 33, 295-310.
    • (1998) Proteins , vol.33 , pp. 295-310
    • Schaffer, L.1    Verkhivker, G.M.2
  • 52
    • 16244403666 scopus 로고    scopus 로고
    • Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach
    • Jenwitheesuk, E.; Samudrala, R. Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. Antivir. Ther. 2005, 10, 157-166.
    • (2005) Antivir. Ther , vol.10 , pp. 157-166
    • Jenwitheesuk, E.1    Samudrala, R.2
  • 53
    • 0034332970 scopus 로고    scopus 로고
    • DARWIN: A program for docking flexible molecules
    • Taylor, J. S.; Burnett, R. M. DARWIN: a program for docking flexible molecules. Proteins 2000, 41, 173-191.
    • (2000) Proteins , vol.41 , pp. 173-191
    • Taylor, J.S.1    Burnett, R.M.2
  • 54
    • 0028491136 scopus 로고
    • GREEN: A program package for docking studies in rational drug design
    • Tomioka, N.; Itai, A. GREEN: a program package for docking studies in rational drug design. J. Comput. Aided Mol. Des. 1994, 8, 347-366.
    • (1994) J. Comput. Aided Mol. Des , vol.8 , pp. 347-366
    • Tomioka, N.1    Itai, A.2
  • 55
    • 0032840569 scopus 로고    scopus 로고
    • DREAM++: Flexible docking program for virtual combinatorial libraries
    • Makino, S.; Ewing, T. J.; Kuntz, I. D. DREAM++: flexible docking program for virtual combinatorial libraries. J. Comput. Aided Mol. Des. 1999, 13, 513-532.
    • (1999) J. Comput. Aided Mol. Des , vol.13 , pp. 513-532
    • Makino, S.1    Ewing, T.J.2    Kuntz, I.D.3
  • 56
    • 34447255356 scopus 로고    scopus 로고
    • D. P. A
    • http://www.bio.vu.nl/nvtb/Docking.html, D. P. A.
  • 58
  • 59
    • 6344245774 scopus 로고    scopus 로고
    • Incorporating protein flexibility in structure-based drug discovery: Using HIV-1 protease as a test case
    • Meagher, K. L.; Carlson, H. A. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. J. Am. Chem. Soc. 2004, 126, 13276-13281.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 13276-13281
    • Meagher, K.L.1    Carlson, H.A.2
  • 60
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-440.
    • (1997) J. Mol. Biol , vol.266 , pp. 424-440
    • Knegtel, R.M.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 61
    • 11144255694 scopus 로고    scopus 로고
    • Evaluation of library ranking efficacy in virtual screening
    • Kontoyianni, M.; Sokol, G. S.; McClellan, L. M. Evaluation of library ranking efficacy in virtual screening. J. Comput. Chem. 2005, 26, 11-22.
    • (2005) J. Comput. Chem , vol.26 , pp. 11-22
    • Kontoyianni, M.1    Sokol, G.S.2    McClellan, L.M.3
  • 62
    • 1942471391 scopus 로고    scopus 로고
    • Assessing scoring functions for protein-ligand interactions
    • Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L. Assessing scoring functions for protein-ligand interactions. J. Med. Chem. 2004, 47, 3032-3047.
    • (2004) J. Med. Chem , vol.47 , pp. 3032-3047
    • Ferrara, P.1    Gohlke, H.2    Price, D.J.3    Klebe, G.4    Brooks, C.L.5
  • 63
    • 0028452628 scopus 로고
    • A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors
    • DesJarlais, R. L.; Dixon, J. S. A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors. J. Comput. Aided Mol. Des. 1994, 8, 231-242.
    • (1994) J. Comput. Aided Mol. Des , vol.8 , pp. 231-242
    • DesJarlais, R.L.1    Dixon, J.S.2
  • 65
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-440.
    • (1997) J. Mol. Biol , vol.266 , pp. 424-440
    • Knegtel, R.M.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 66
    • 0037402655 scopus 로고    scopus 로고
    • Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases
    • Joseph-McCarthy, D.; Alvarez, J. C. Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases. Proteins 2003, 51, 189-202.
    • (2003) Proteins , vol.51 , pp. 189-202
    • Joseph-McCarthy, D.1    Alvarez, J.C.2
  • 68
    • 22144485942 scopus 로고    scopus 로고
    • Enhancing the accuracy of virtual screening: Molecular dynamics with quantum-refined force fields
    • Curioni, A.; Mordasini, T.; Andreoni, W. Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields. J. Comput. Aided Mol. Des. 2004 18, 773-784.
    • (2004) J. Comput. Aided Mol. Des , vol.18 , pp. 773-784
    • Curioni, A.1    Mordasini, T.2    Andreoni, W.3
  • 69
    • 22244451417 scopus 로고    scopus 로고
    • Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes
    • Raha, K.; Merz, K. M., Jr. Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J. Med. Chem. 2005, 48, 4558-4575.
    • (2005) J. Med. Chem , vol.48 , pp. 4558-4575
    • Raha, K.1    Merz Jr., K.M.2
  • 70
    • 7444257387 scopus 로고    scopus 로고
    • Efficient evaluation of binding free energy using continuum electrostatics solvation
    • Huang, D.; Caflisch, A. Efficient evaluation of binding free energy using continuum electrostatics solvation. J. Med. Chem. 2004, 47, 5791-5797.
    • (2004) J. Med. Chem , vol.47 , pp. 5791-5797
    • Huang, D.1    Caflisch, A.2
  • 71
    • 23944499528 scopus 로고    scopus 로고
    • Improving binding mode predictions by docking into protein-specifically adapted potential fields
    • Radestock, S.; Bohm, M.; Gohlke, H. Improving binding mode predictions by docking into protein-specifically adapted potential fields. J. Med. Chem. 2005, 48, 5466-5479.
    • (2005) J. Med. Chem , vol.48 , pp. 5466-5479
    • Radestock, S.1    Bohm, M.2    Gohlke, H.3
  • 72
    • 10044254671 scopus 로고    scopus 로고
    • Application of machine learning to improve the results of high-throughput docking against the HIV-1 protease
    • Klon, A. E.; Glick, M.; Davies, J. W. Application of machine learning to improve the results of high-throughput docking against the HIV-1 protease. J. Chem. Inf. Comput. Sci. 2004, 44, 2216-2224.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 2216-2224
    • Klon, A.E.1    Glick, M.2    Davies, J.W.3
  • 73
    • 22444448408 scopus 로고    scopus 로고
    • Virtual screening for anti-HIV-1 RT and anti-HIV-1 PR inhibitors from the Thai medicinal plants database: A combined docking with neural networks approach
    • Sangma, C.; Chuakheaw, D.; Jongkon, N.; Saenbandit, K.; Nunrium, P.; Uthayopas, P.; Hannongbua, S. Virtual screening for anti-HIV-1 RT and anti-HIV-1 PR inhibitors from the Thai medicinal plants database: a combined docking with neural networks approach. Comb. Chem. High Throughput Screen 2005, 8, 417-429.
    • (2005) Comb. Chem. High Throughput Screen , vol.8 , pp. 417-429
    • Sangma, C.1    Chuakheaw, D.2    Jongkon, N.3    Saenbandit, K.4    Nunrium, P.5    Uthayopas, P.6    Hannongbua, S.7
  • 74
    • 0001074001 scopus 로고    scopus 로고
    • Handbook of Molecular Descriptors
    • Mannold, R, Kubinyi, H, Timmerman, H, Eds, Wiley-VCH: Weinheim and New York
    • Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors. In Methods and Principles in Medicinal Chemistry Series; Mannold, R.; Kubinyi, H.; Timmerman, H.; Eds.; Wiley-VCH: Weinheim and New York, 2000.
    • (2000) Methods and Principles in Medicinal Chemistry Series
    • Todeschini, R.1    Consonni, V.2
  • 75
    • 0033779243 scopus 로고    scopus 로고
    • Molecular Descriptors in Chemoinformatics, Computational Combinatorial Chemistry, and Virtual Screening
    • Xue, L.; Bajorath, J. Molecular Descriptors in Chemoinformatics, Computational Combinatorial Chemistry, and Virtual Screening. Combinatorial Chemistry & High Throughput Screening 2000, 3, 363-372.
    • (2000) Combinatorial Chemistry & High Throughput Screening , vol.3 , pp. 363-372
    • Xue, L.1    Bajorath, J.2
  • 76
    • 0035003411 scopus 로고    scopus 로고
    • Identification of the descriptor pharmacophores using variable selection QSAR: Applications to database mining
    • Tropsha, A.; Zheng, W. Identification of the descriptor pharmacophores using variable selection QSAR: applications to database mining. Curr. Pharm. Des. 2001, 7, 599-612.
    • (2001) Curr. Pharm. Des , vol.7 , pp. 599-612
    • Tropsha, A.1    Zheng, W.2
  • 77
    • 0016568865 scopus 로고
    • A method of structure-activity correlation using Wiswesser Line Notation
    • Adamson, G. W.; Bawden, D. A method of structure-activity correlation using Wiswesser Line Notation. J. Chem. Inf. Comput. Sci. 1975, 15, 215-220.
    • (1975) J. Chem. Inf. Comput. Sci , vol.15 , pp. 215-220
    • Adamson, G.W.1    Bawden, D.2
  • 78
    • 0017522257 scopus 로고
    • A substructural analysis method for structure-activity correlation of heterocyclic compounds using Wiswesser line notation
    • Adamson, G. W.; Bawden, D. A substructural analysis method for structure-activity correlation of heterocyclic compounds using Wiswesser line notation. J. Chem. Inf. Comput. Sci. 1977, 17, 164-171.
    • (1977) J. Chem. Inf. Comput. Sci , vol.17 , pp. 164-171
    • Adamson, G.W.1    Bawden, D.2
  • 79
    • 0023965741 scopus 로고    scopus 로고
    • Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
    • Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
  • 82
    • 0036429879 scopus 로고    scopus 로고
    • Kotani, T. H.; K. Rapid Evaluation of Molecular Shape Similarity Index Using Pairwise Calculation of the Nearest Atomic Distances J. Chem. Inf. Comput. Sci. 2002, 42, 58-63.
    • Kotani, T. H.; K. Rapid Evaluation of Molecular Shape Similarity Index Using Pairwise Calculation of the Nearest Atomic Distances J. Chem. Inf. Comput. Sci. 2002, 42, 58-63.
  • 83
    • 0038722927 scopus 로고    scopus 로고
    • Similarity Searching in Databases of Flexible 3D Structures Using Smoothed Bounded Distance Matrices
    • Raymond, J. W.; Willett, P. Similarity Searching in Databases of Flexible 3D Structures Using Smoothed Bounded Distance Matrices. J. Chem. Inf. Comput. Sci. 2003, 43, 908-916.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 908-916
    • Raymond, J.W.1    Willett, P.2
  • 84
    • 14044279262 scopus 로고    scopus 로고
    • Le, S. Y. M., J. V. Jr.; Zhang, K. In An algorithm for detecting homologues of known structured RNAs in genomes., Proc IEEE Comput Syst Bioinform Conf, 2004.
    • Le, S. Y. M., J. V. Jr.; Zhang, K. In An algorithm for detecting homologues of known structured RNAs in genomes., Proc IEEE Comput Syst Bioinform Conf, 2004.
  • 85
    • 33644615306 scopus 로고    scopus 로고
    • Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations
    • Park, S. H. R., K. H.; Gilbert D. Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations. Int. J. Neural. Syst. 2005, 15, 287-296.
    • (2005) Int. J. Neural. Syst , vol.15 , pp. 287-296
    • Park, S.H.R.K.H.1    Gilbert, D.2
  • 86
    • 0037313495 scopus 로고    scopus 로고
    • Mini-fingerprints for virtual screening: Design principles and generation of novel prototypes based on information theory
    • Xue, L.; Godden, J. W.; Bajorath, J. Mini-fingerprints for virtual screening: design principles and generation of novel prototypes based on information theory. SAR QSAR Environ. Res. 2003, 14, 27-40.
    • (2003) SAR QSAR Environ. Res , vol.14 , pp. 27-40
    • Xue, L.1    Godden, J.W.2    Bajorath, J.3
  • 88
    • 0038170311 scopus 로고    scopus 로고
    • Similarity Metrics for Ligands. Reflecting the Similarity of the Target Proteins
    • Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. Similarity Metrics for Ligands. Reflecting the Similarity of the Target Proteins. J. Chem. Inf. Comput. Sci. 2003, 43, 391-405.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 391-405
    • Schuffenhauer, A.1    Floersheim, P.2    Acklin, P.3    Jacoby, E.4
  • 89
    • 0036489451 scopus 로고    scopus 로고
    • Fang, X. W., S. A Web-Based 3D-Database Pharmacophore Searching Tool for Drug Discovery J. Chem. Inf. Comput. Sci. 2002, 42, 192-198.
    • Fang, X. W., S. A Web-Based 3D-Database Pharmacophore Searching Tool for Drug Discovery J. Chem. Inf. Comput. Sci. 2002, 42, 192-198.
  • 92
    • 33751392117 scopus 로고
    • Clustering of chemical structures on the basis of two-dimensional similarity measures
    • Barnard, J. M.; Downs, G. M. Clustering of chemical structures on the basis of two-dimensional similarity measures. J. Chem. Inf. Comput. Sci. 1992, 32, 644-649.
    • (1992) J. Chem. Inf. Comput. Sci , vol.32 , pp. 644-649
    • Barnard, J.M.1    Downs, G.M.2
  • 93
    • 0035960060 scopus 로고    scopus 로고
    • Quantitative Structure-Antitumor Activity Relationships of Camptothecin Analogues: Cluster Analysis and Genetic Algorithm-Based Studies
    • Fan, Y.; Shi, L. M.; Kohn, K. W.; Pommier, Y.; Weinstein, J. N. Quantitative Structure-Antitumor Activity Relationships of Camptothecin Analogues: Cluster Analysis and Genetic Algorithm-Based Studies. J. Med. Chem. 2001, 44, 3254-3263.
    • (2001) J. Med. Chem , vol.44 , pp. 3254-3263
    • Fan, Y.1    Shi, L.M.2    Kohn, K.W.3    Pommier, Y.4    Weinstein, J.N.5
  • 94
    • 0342645323 scopus 로고    scopus 로고
    • Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection
    • Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
    • (1996) J. Chem. Inf. Comput. Sci , vol.36 , pp. 572-584
    • Brown, R.D.1    Martin, Y.C.2
  • 95
    • 0023074807 scopus 로고
    • Cluster significance analysis contrasted with three other quantitative structure-activity relationship methods
    • McFarland, J. W.; Gans, D. J. Cluster significance analysis contrasted with three other quantitative structure-activity relationship methods. J. Med. Chem. 1987, 30, 46-49.
    • (1987) J. Med. Chem , vol.30 , pp. 46-49
    • McFarland, J.W.1    Gans, D.J.2
  • 96
    • 0037248697 scopus 로고    scopus 로고
    • Predicting HIV drug resistance with neural networks
    • Draghici, S.; Potter, R. B. Predicting HIV drug resistance with neural networks. Bioinformatics 2003, 19, 98-107.
    • (2003) Bioinformatics , vol.19 , pp. 98-107
    • Draghici, S.1    Potter, R.B.2
  • 97
    • 0042856583 scopus 로고    scopus 로고
    • Classification of HIV protease inhibitors on the basis of their antiviral potency using radial basis function neural networks
    • Patankar, S. J.; Jurs, P. C. Classification of HIV protease inhibitors on the basis of their antiviral potency using radial basis function neural networks. J. Comput. Aided Mol. Des. 2003, 17, 155-171.
    • (2003) J. Comput. Aided Mol. Des , vol.17 , pp. 155-171
    • Patankar, S.J.1    Jurs, P.C.2
  • 98
    • 0035263413 scopus 로고    scopus 로고
    • Similarity Calculations Using Two-Dimensional Molecular Representations
    • Allen, B. C. P.; Grant G. H.; Richards, W. G. Similarity Calculations Using Two-Dimensional Molecular Representations. J. Chem. Inf. Comput. Sci. 2001, 41, 330-337.
    • (2001) J. Chem. Inf. Comput. Sci , vol.41 , pp. 330-337
    • Allen, B.C.P.1    Grant, G.H.2    Richards, W.G.3
  • 99
    • 2342565108 scopus 로고    scopus 로고
    • Prediction of biological targets using probabilistic neural networks and atom-type descriptors
    • Niwa, T. Prediction of biological targets using probabilistic neural networks and atom-type descriptors. J. Med. Chem. 2004, 47, 2645-2650.
    • (2004) J. Med. Chem , vol.47 , pp. 2645-2650
    • Niwa, T.1


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