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Volumn 49, Issue 6, 2009, Pages 1558-1567

Molecular insights into 14-membered macrolides using the MM-PBSA method

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTICS; FREE ENERGY; MOLECULAR DYNAMICS; VAN DER WAALS FORCES;

EID: 67650035452     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci8003495     Document Type: Article
Times cited : (17)

References (59)
  • 1
    • 33644921212 scopus 로고    scopus 로고
    • A journey across the sequential development of macrolides and ketolides related to erythromycin
    • Pal, S. A journey across the sequential development of macrolides and ketolides related to erythromycin. Tetrahedron 2006, 62 (14), 3171-3200.
    • (2006) Tetrahedron , vol.62 , Issue.14 , pp. 3171-3200
    • Pal, S.1
  • 2
    • 0036782870 scopus 로고    scopus 로고
    • Ketolides: The future of the macrolides
    • Nilius, A. M.; Ma, Z. Ketolides: the future of the macrolides. Curr. Opin. Pharmacol. 2002, 2 (5), 493-500.
    • (2002) Curr. Opin. Pharmacol , vol.2 , Issue.5 , pp. 493-500
    • Nilius, A.M.1    Ma, Z.2
  • 3
    • 0026021209 scopus 로고
    • New ether oxime derivatives of erythromycin A. A structure-activity relationship study
    • Gasc, J. C.; d'Ambrieres, S. G.; Lutz, A.; Chantot, J. F. New ether oxime derivatives of erythromycin A. A structure-activity relationship study. J. Antibiot. (Tokyo) 1991, 44 (3), 313-330.
    • (1991) J. Antibiot. (Tokyo) , vol.44 , Issue.3 , pp. 313-330
    • Gasc, J.C.1    d'Ambrieres, S.G.2    Lutz, A.3    Chantot, J.F.4
  • 5
    • 0032479332 scopus 로고    scopus 로고
    • Analysis of macrolide antibiotics
    • Kanfer, I.; Skinner, M. F.; Walker, R. B. Analysis of macrolide antibiotics. J. Chromatogr., A 1998, 812 (1-2), 255-286.
    • (1998) J. Chromatogr., A , vol.812 , Issue.1-2 , pp. 255-286
    • Kanfer, I.1    Skinner, M.F.2    Walker, R.B.3
  • 6
    • 0034115717 scopus 로고    scopus 로고
    • Macrolide-ketolide inhibition of MLS-resistant ribosomes is improved by alternative drug interaction with domain II of 23S rRNA
    • Douthwaite, S.; Hansen, L. H.; Mauvais, P. Macrolide-ketolide inhibition of MLS-resistant ribosomes is improved by alternative drug interaction with domain II of 23S rRNA. Mol. Microbiol. 2000, 36 (1), 183-193.
    • (2000) Mol. Microbiol , vol.36 , Issue.1 , pp. 183-193
    • Douthwaite, S.1    Hansen, L.H.2    Mauvais, P.3
  • 7
    • 0035950132 scopus 로고    scopus 로고
    • Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria
    • Schlunzen, F.; Zarivach, R.; Harms, J.; Bashan, A.; Tocilj, A.; Albrecht, R.; Yonath, A.; Franceschi, F. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 2001, 413 (6858), 814-821.
    • (2001) Nature , vol.413 , Issue.6858 , pp. 814-821
    • Schlunzen, F.1    Zarivach, R.2    Harms, J.3    Bashan, A.4    Tocilj, A.5    Albrecht, R.6    Yonath, A.7    Franceschi, F.8
  • 8
    • 0032904341 scopus 로고    scopus 로고
    • A ketolide resistance mutation in domain II of 23S rRNA reveals the proximity of hairpin 35 to the peptidyl transferase centre
    • Xiong, L.; Shah, S.; Mauvais, P.; Mankin, A. S. A ketolide resistance mutation in domain II of 23S rRNA reveals the proximity of hairpin 35 to the peptidyl transferase centre. Mol. Microbiol. 1999, 31 (2), 633-639.
    • (1999) Mol. Microbiol , vol.31 , Issue.2 , pp. 633-639
    • Xiong, L.1    Shah, S.2    Mauvais, P.3    Mankin, A.S.4
  • 9
    • 0032950956 scopus 로고    scopus 로고
    • The macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA
    • Hansen, L. H.; Mauvais, P.; Douthwaite, S. The macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA. Mol. Microbiol. 1999, 31 (2), 623-631.
    • (1999) Mol. Microbiol , vol.31 , Issue.2 , pp. 623-631
    • Hansen, L.H.1    Mauvais, P.2    Douthwaite, S.3
  • 10
    • 0028914553 scopus 로고
    • Insights into erythromycin action from studies of its activity as inducer of resistance
    • Weisblum, B. Insights into erythromycin action from studies of its activity as inducer of resistance. Antimicrob. Agents Chemother. 1995, 39 (4), 797-805.
    • (1995) Antimicrob. Agents Chemother , vol.39 , Issue.4 , pp. 797-805
    • Weisblum, B.1
  • 11
    • 0035160878 scopus 로고    scopus 로고
    • Macrolide resistance conferred by base substitutions in 23S rRNA
    • Vester, B.; Douthwaite, S. Macrolide resistance conferred by base substitutions in 23S rRNA. Antimicrob. Agents Chemother. 2001, 45 (1), 1-12.
    • (2001) Antimicrob. Agents Chemother , vol.45 , Issue.1 , pp. 1-12
    • Vester, B.1    Douthwaite, S.2
  • 12
    • 11244307407 scopus 로고    scopus 로고
    • Binding site of the bridged macrolides in the Escherichia coli ribosome
    • Xiong, L.; Korkhin, Y.; Mankin, A. S. Binding site of the bridged macrolides in the Escherichia coli ribosome. Antimicrob. Agents Chemother. 2005, 49 (1), 281-288.
    • (2005) Antimicrob. Agents Chemother , vol.49 , Issue.1 , pp. 281-288
    • Xiong, L.1    Korkhin, Y.2    Mankin, A.S.3
  • 13
    • 47949091443 scopus 로고    scopus 로고
    • Refinement of a Low-resolution Crystal Structure to Better Understand Erythromycin Interactions on Large Ribosomal Subunit
    • Wahab, H. A.; Yam, W. K.; Samian, M. R.; Najimudin, N. Refinement of a Low-resolution Crystal Structure to Better Understand Erythromycin Interactions on Large Ribosomal Subunit. J. Biomol. Struct. Dyn. 2008, 26 (1), 131-146.
    • (2008) J. Biomol. Struct. Dyn , vol.26 , Issue.1 , pp. 131-146
    • Wahab, H.A.1    Yam, W.K.2    Samian, M.R.3    Najimudin, N.4
  • 14
    • 0016114678 scopus 로고
    • Effect of erythromycin analogues on binding of [14C]erythromycin to Escherichia coli ribosomes
    • Pestka, S.; Lemahieu, R. A. Effect of erythromycin analogues on binding of [14C]erythromycin to Escherichia coli ribosomes. Antimicrob. Agents Chemother. 1974, 6 (4), 479-488.
    • (1974) Antimicrob. Agents Chemother , vol.6 , Issue.4 , pp. 479-488
    • Pestka, S.1    Lemahieu, R.A.2
  • 15
    • 0027248565 scopus 로고
    • Erythromycin binding is reduced in ribosomes with conformational alterations in the 23 S rRNA peptidyl transferase loop
    • Douthwaite, S.; Aagaard, C. Erythromycin binding is reduced in ribosomes with conformational alterations in the 23 S rRNA peptidyl transferase loop. J. Mol. Biol. 1993, 232 (3), 725-731.
    • (1993) J. Mol. Biol , vol.232 , Issue.3 , pp. 725-731
    • Douthwaite, S.1    Aagaard, C.2
  • 16
    • 0344406768 scopus 로고    scopus 로고
    • Erythromycin, roxithromycin, and clarithromycin: Use of slow-binding kinetics to compare their in vitro interaction with a bacterial ribosomal complex active in peptide bond formation
    • Dinos, G. P.; Connell, S. R.; Nierhaus, K. H.; Kalpaxis, D. L. Erythromycin, roxithromycin, and clarithromycin: use of slow-binding kinetics to compare their in vitro interaction with a bacterial ribosomal complex active in peptide bond formation. Mol. Pharmacol. 2003, 63 (3), 617-623.
    • (2003) Mol. Pharmacol , vol.63 , Issue.3 , pp. 617-623
    • Dinos, G.P.1    Connell, S.R.2    Nierhaus, K.H.3    Kalpaxis, D.L.4
  • 17
    • 11144238888 scopus 로고    scopus 로고
    • Kinetics of macrolide action: The josamycin and erythromycin cases
    • Lovmar, M.; Tenson, T.; Ehrenberg, M. Kinetics of macrolide action: the josamycin and erythromycin cases. J. Biol. Chem. 2004, 279 (51), 53506-53515.
    • (2004) J. Biol. Chem , vol.279 , Issue.51 , pp. 53506-53515
    • Lovmar, M.1    Tenson, T.2    Ehrenberg, M.3
  • 18
    • 0034521981 scopus 로고    scopus 로고
    • Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. 3rd. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33 (12), 889-897.
    • Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. 3rd. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33 (12), 889-897.
  • 19
    • 6344247347 scopus 로고    scopus 로고
    • MMPBSA applied to computer-assisted ligand design
    • Rami Reddy, M, Erion, M. D, Eds, Kluwer Academic/Plenum Publishers: New York
    • Kuhn, B.; Donini, O.; Huo, S.; Wang, J. M.; Kollman, P. A. MMPBSA applied to computer-assisted ligand design. In Free energy calculations in rational drug design; Rami Reddy, M.; Erion, M. D., Eds.; Kluwer Academic/Plenum Publishers: New York, 2001; pp 243-251.
    • (2001) Free energy calculations in rational drug design , pp. 243-251
    • Kuhn, B.1    Donini, O.2    Huo, S.3    Wang, J.M.4    Kollman, P.A.5
  • 21
    • 0029011701 scopus 로고    scopus 로고
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; W., C. J.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; W., C. J.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
  • 22
  • 23
    • 67650041469 scopus 로고    scopus 로고
    • Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A. J, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Lyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Klene, M, Li, X, Knox, J. E, Hratchian, H. P, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, train, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Martin, R. L, Fox, D. J, Keith
    • Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A. J.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Lyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; train, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02.; Gaussian, Inc.: Wallingford, CT, 2004.
  • 24
    • 67650041470 scopus 로고    scopus 로고
    • Wang, J. M.; Wang, W.; Kollman, P. A. Antechamber: An accessory software package for molecular mechanical calculations. Abstr. Pap. Am. Chem. Soc. 2001, 222, U403-U403.
    • Wang, J. M.; Wang, W.; Kollman, P. A. Antechamber: An accessory software package for molecular mechanical calculations. Abstr. Pap. Am. Chem. Soc. 2001, 222, U403-U403.
  • 25
    • 28944431876 scopus 로고    scopus 로고
    • Development and validation of empirical force field parameters for netropsin
    • Bren, U.; Hodoscek, M.; Koller, J. Development and validation of empirical force field parameters for netropsin. J. Chem. Inf. Model. 2005, 45 (6), 1546-1552.
    • (2005) J. Chem. Inf. Model , vol.45 , Issue.6 , pp. 1546-1552
    • Bren, U.1    Hodoscek, M.2    Koller, J.3
  • 28
    • 84952104504 scopus 로고    scopus 로고
    • Pastor, R. W.; Brooks, B. R.; A., S. An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol. Phys. 1988, 65, 1409-1419.
    • Pastor, R. W.; Brooks, B. R.; A., S. An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol. Phys. 1988, 65, 1409-1419.
  • 29
    • 32844457567 scopus 로고
    • Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models
    • Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98 (7), 1978-1988.
    • (1994) J. Phys. Chem , vol.98 , Issue.7 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 30
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
    • Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. J. Comput. Chem. 2002, 23 (1), 128-137.
    • (2002) J. Comput. Chem , vol.23 , Issue.1 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 31
    • 33751385054 scopus 로고
    • Macroscopic Models of Aqueous-Solutions - Biological and Chemical Applications
    • Honig, B.; Sharp, K.; Yang, A. S. Macroscopic Models of Aqueous-Solutions - Biological and Chemical Applications. J. Phys. Chem. 1993, 97 (6), 1101-1109.
    • (1993) J. Phys. Chem , vol.97 , Issue.6 , pp. 1101-1109
    • Honig, B.1    Sharp, K.2    Yang, A.S.3
  • 32
    • 0021470624 scopus 로고
    • Buried Surface-Area, Conformational Entropy, and Protein Stability
    • Rashin, A. A. Buried Surface-Area, Conformational Entropy, and Protein Stability. Biopolymers 1984, 23 (8), 1605-1620.
    • (1984) Biopolymers , vol.23 , Issue.8 , pp. 1605-1620
    • Rashin, A.A.1
  • 33
    • 0033405041 scopus 로고    scopus 로고
    • Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
    • Chong, L. T.; Duan, Y.; Wang, L.; Massova, I.; Kollman, P. A. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc. Natl. Acad. Sci. U. S. A. 1999, 96 (25), 14330-14335.
    • (1999) Proc. Natl. Acad. Sci. U. S. A , vol.96 , Issue.25 , pp. 14330-14335
    • Chong, L.T.1    Duan, Y.2    Wang, L.3    Massova, I.4    Kollman, P.A.5
  • 34
    • 0034646574 scopus 로고    scopus 로고
    • Structure and thermodynamics of RNA-protein binding: Using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change
    • Reyes, C. M.; Kollman, P. A. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J. Mol. Biol. 2000, 297 (5), 1145-1158.
    • (2000) J. Mol. Biol , vol.297 , Issue.5 , pp. 1145-1158
    • Reyes, C.M.1    Kollman, P.A.2
  • 35
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 2001, 123 (22), 5221-5230.
    • (2001) J. Am. Chem. Soc , vol.123 , Issue.22 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 36
    • 0031788539 scopus 로고    scopus 로고
    • Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
    • Cheatham, T. E., 3rd; Srinivasan, J.; Case, D. A.; Kollman, P. A. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 1998, 16 (2), 265-280.
    • (1998) J. Biomol. Struct. Dyn , vol.16 , Issue.2 , pp. 265-280
    • Cheatham 3rd, T.E.1    Srinivasan, J.2    Case, D.A.3    Kollman, P.A.4
  • 38
    • 0038811884 scopus 로고    scopus 로고
    • Bacterial ribosomal subunit assembly is an antibiotic target
    • Champney, W. S. Bacterial ribosomal subunit assembly is an antibiotic target. Curr. Top. Med. Chem. 2003, 3 (9), 929-947.
    • (2003) Curr. Top. Med. Chem , vol.3 , Issue.9 , pp. 929-947
    • Champney, W.S.1
  • 40
    • 0031837381 scopus 로고    scopus 로고
    • Transferred nuclear Overhauser effect study of macrolide-ribosome interactions: Correlation between antibiotic activities and bound conformations
    • Bertho, G.; Gharbi-Benarous, J.; Delaforge, M.; Girault, J. P. Transferred nuclear Overhauser effect study of macrolide-ribosome interactions: correlation between antibiotic activities and bound conformations. Bioorg. Med. Chem. 1998, 6 (2), 209-221.
    • (1998) Bioorg. Med. Chem , vol.6 , Issue.2 , pp. 209-221
    • Bertho, G.1    Gharbi-Benarous, J.2    Delaforge, M.3    Girault, J.P.4
  • 41
    • 1842866544 scopus 로고    scopus 로고
    • Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations
    • Otyepka, M.; Kriz, Z.; Koca, J. Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations. J. Biomol. Struct. Dyn. 2002, 20 (2), 141-154.
    • (2002) J. Biomol. Struct. Dyn , vol.20 , Issue.2 , pp. 141-154
    • Otyepka, M.1    Kriz, Z.2    Koca, J.3
  • 42
    • 23844553757 scopus 로고    scopus 로고
    • T315I-mutated Bcr-Abl in chronic myeloid leukemia and imatinib: Insights from a computational study
    • Pricl, S.; Fermeglia, M.; Ferrone, M.; Tamborini, E. T315I-mutated Bcr-Abl in chronic myeloid leukemia and imatinib: insights from a computational study. Mol. Cancer Ther. 2005, 4 (8), 1167-1174.
    • (2005) Mol. Cancer Ther , vol.4 , Issue.8 , pp. 1167-1174
    • Pricl, S.1    Fermeglia, M.2    Ferrone, M.3    Tamborini, E.4
  • 43
    • 31344452474 scopus 로고    scopus 로고
    • Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods
    • Adekoya, O. A.; Willassen, N. P.; Sylte, I. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods. J. Struct. Biol. 2006, 153 (2), 129-144.
    • (2006) J. Struct. Biol , vol.153 , Issue.2 , pp. 129-144
    • Adekoya, O.A.1    Willassen, N.P.2    Sylte, I.3
  • 44
    • 33748442331 scopus 로고    scopus 로고
    • A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method
    • Xu, Y.; Wang, R. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method. Proteins 2006, 64 (4), 1058-1068.
    • (2006) Proteins , vol.64 , Issue.4 , pp. 1058-1068
    • Xu, Y.1    Wang, R.2
  • 45
    • 33749002274 scopus 로고    scopus 로고
    • Impact of EGFR point mutations on the sensitivity to gefitinib: Insights from comparative structural analyses and molecular dynamics simulations
    • Liu, B.; Bernard, B.; Wu, J. H. Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations. Proteins 2006, 65 (2), 331-346.
    • (2006) Proteins , vol.65 , Issue.2 , pp. 331-346
    • Liu, B.1    Bernard, B.2    Wu, J.H.3
  • 46
    • 0037234043 scopus 로고    scopus 로고
    • Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
    • Gouda, H.; Kuntz, I. D.; Case, D. A.; Kollman, P. A. Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 2003, 68 (1), 16-34.
    • (2003) Biopolymers , vol.68 , Issue.1 , pp. 16-34
    • Gouda, H.1    Kuntz, I.D.2    Case, D.A.3    Kollman, P.A.4
  • 47
    • 33751237378 scopus 로고    scopus 로고
    • Can MM-PBSA calculations predict the specificities of protein kinase inhibitors
    • Page, C. S.; Bates, P. A. Can MM-PBSA calculations predict the specificities of protein kinase inhibitors. J. Comput. Chem. 2006, 27 (16), 1990-2007.
    • (2006) J. Comput. Chem , vol.27 , Issue.16 , pp. 1990-2007
    • Page, C.S.1    Bates, P.A.2
  • 48
    • 20444377245 scopus 로고    scopus 로고
    • Validation and use of the MM-PBSA approach for drug discovery
    • Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and use of the MM-PBSA approach for drug discovery. J. Med. Chem. 2005, 48 (12), 4040-4048.
    • (2005) J. Med. Chem , vol.48 , Issue.12 , pp. 4040-4048
    • Kuhn, B.1    Gerber, P.2    Schulz-Gasch, T.3    Stahl, M.4
  • 49
    • 33947495228 scopus 로고    scopus 로고
    • Do all pieces make a whole? Thiele cumulants and the free energy decomposition
    • Bren, M.; Florian, J.; Mavri, J.; Bren, U. Do all pieces make a whole? Thiele cumulants and the free energy decomposition. Theor. Chem. Acc. 2007, 117 (4), 535-540.
    • (2007) Theor. Chem. Acc , vol.117 , Issue.4 , pp. 535-540
    • Bren, M.1    Florian, J.2    Mavri, J.3    Bren, U.4
  • 50
    • 33746508990 scopus 로고    scopus 로고
    • Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method
    • Bren, U.; Martinek, V.; Florian, J. Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method. J. Phys. Chem. B 2006, 110 (25), 12782-12788.
    • (2006) J. Phys. Chem. B , vol.110 , Issue.25 , pp. 12782-12788
    • Bren, U.1    Martinek, V.2    Florian, J.3
  • 51
    • 22244433549 scopus 로고    scopus 로고
    • Antibiotics targeting ribosomes: Resistance, selectivity, synergism, and cellular regulation
    • Yonath, A. Antibiotics targeting ribosomes: resistance, selectivity, synergism, and cellular regulation. Annu. Rev. Biochem. 2005, 74, 649-679.
    • (2005) Annu. Rev. Biochem , vol.74 , pp. 649-679
    • Yonath, A.1
  • 52
    • 0023604799 scopus 로고
    • Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA
    • Moazed, D.; Noller, H. F. Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie 1987, 69 (8), 879-884.
    • (1987) Biochimie , vol.69 , Issue.8 , pp. 879-884
    • Moazed, D.1    Noller, H.F.2
  • 53
    • 0034817784 scopus 로고    scopus 로고
    • Short peptides conferring resistance to macrolide antibiotics
    • Tenson, T.; Mankin, A. S. Short peptides conferring resistance to macrolide antibiotics. Peptides 2001, 22 (10), 1661-1668.
    • (2001) Peptides , vol.22 , Issue.10 , pp. 1661-1668
    • Tenson, T.1    Mankin, A.S.2
  • 54
    • 17444421169 scopus 로고    scopus 로고
    • Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance
    • Tu, D.; Blaha, G.; Moore, P. B.; Steitz, T. A. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 2005, 121 (2), 257-270.
    • (2005) Cell , vol.121 , Issue.2 , pp. 257-270
    • Tu, D.1    Blaha, G.2    Moore, P.B.3    Steitz, T.A.4
  • 55
    • 4444300505 scopus 로고    scopus 로고
    • The structural basis of macrolide-ribosome binding assessed using mutagenesis of 23S rRNA positions 2058 and 2059
    • Pfister, P.; Jenni, S.; Poehlsgaard, J.; Thomas, A.; Douthwaite, S.; Ban, N.; Bottger, E. C. The structural basis of macrolide-ribosome binding assessed using mutagenesis of 23S rRNA positions 2058 and 2059. J. Mol. Biol. 2004, 342 (5), 1569-1581.
    • (2004) J. Mol. Biol , vol.342 , Issue.5 , pp. 1569-1581
    • Pfister, P.1    Jenni, S.2    Poehlsgaard, J.3    Thomas, A.4    Douthwaite, S.5    Ban, N.6    Bottger, E.C.7
  • 56
    • 0036716799 scopus 로고    scopus 로고
    • Resistance to macrolides and related antibiotics in Streptococcus pneumoniae
    • Leclercq, R.; Courvalin, P. Resistance to macrolides and related antibiotics in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 2002, 46 (9), 2727-2734.
    • (2002) Antimicrob. Agents Chemother , vol.46 , Issue.9 , pp. 2727-2734
    • Leclercq, R.1    Courvalin, P.2
  • 58
    • 4244087787 scopus 로고
    • Molecular dynamics and free energy calculations applied to the enzyme barnase and one of its stability mutants
    • Goodfellow, J. M, Ed, VCH: Weinheim, New York
    • Wodak, S. J.; Belle, D. v.; Prevost, M. Molecular dynamics and free energy calculations applied to the enzyme barnase and one of its stability mutants. In Computer Modelling in Molecular Biology; Goodfellow, J. M., Ed.; VCH: Weinheim, New York, 1995; pp 62-102.
    • (1995) Computer Modelling in Molecular Biology , pp. 62-102
    • Wodak, S.J.1    Belle, D.V.2    Prevost, M.3
  • 59
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey, W.; Dalke, A.; Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 1996, 14 (1), 27-38.
    • (1996) J. Mol. Graph , vol.14 , Issue.1 , pp. 27-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3


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