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Volumn 50, Issue 12, 2010, Pages 2236-2247

Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRAL AGENTS; DRUG THERAPY; GLYCOPROTEINS; LIGANDS; MOLECULAR DYNAMICS; VAN DER WAALS FORCES; VIRUSES;

EID: 78650686774     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100346s     Document Type: Article
Times cited : (76)

References (91)
  • 1
    • 0019119577 scopus 로고
    • A revision of the system of nomenclature for influenza viruses: A WHO memorandum
    • WHO
    • WHO A revision of the system of nomenclature for influenza viruses: A WHO memorandum Bull. W. H. O. 1980, 58, 585-591
    • (1980) Bull. W. H. O. , vol.58 , pp. 585-591
  • 2
  • 4
    • 0035137605 scopus 로고    scopus 로고
    • Pandemic threat posed by avian influenza A viruses
    • Taisuke, H.; Kawaoka, Y. Pandemic threat posed by avian influenza A viruses Clin. Microbiol. Rev. Soc. 2001, 14, 129-149
    • (2001) Clin. Microbiol. Rev. Soc. , vol.14 , pp. 129-149
    • Taisuke, H.1    Kawaoka, Y.2
  • 5
    • 78650709210 scopus 로고    scopus 로고
    • WHO. Pandemic (H1N1) 2009, briefing note 4, (accessed July 24, 2009).
    • WHO. Pandemic (H1N1) 2009, briefing note 4, http://www.who.int/csr/ disease/swineflu/notes/h1n1ituation0090724/en/index.html (accessed July 24, 2009).
  • 7
    • 27144468290 scopus 로고    scopus 로고
    • Avian flu: Isolation of drug-resistant H5N1 virus
    • Le, Q. M. Avian flu: Isolation of drug-resistant H5N1 virus Nature 2005, 437, 1108
    • (2005) Nature , vol.437 , pp. 1108
    • Le, Q.M.1
  • 8
    • 33751231111 scopus 로고    scopus 로고
    • H5N1 influenza-continuing evolution and spread
    • Webster, R. G.; Govorkova, E. A. H5N1 influenza-continuing evolution and spread N. Engl. J. Med. 2006, 355, 2174-2177
    • (2006) N. Engl. J. Med. , vol.355 , pp. 2174-2177
    • Webster, R.G.1    Govorkova, E.A.2
  • 11
    • 78650714072 scopus 로고    scopus 로고
    • Wkly Epidemiol Rec, Pandemic (H1N1) 2009, briefing note 1 Virus resistant to oseltamivir (tamiflu) identified, (accessed July 8, 2009).
    • Wkly Epidemiol Rec, Pandemic (H1N1) 2009, briefing note 1 Virus resistant to oseltamivir (tamiflu) identified, http://www.who.int/csr/disease/swineflu/ notes/h1n1ntiviralesistance0090708/en/index.html, (accessed July 8, 2009).
  • 12
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, J. A. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase J. Med. Chem. 2008, 51, 3878-3894
    • (2008) J. Med. Chem. , vol.51 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5    McCammon, J.A.6
  • 13
    • 14844293471 scopus 로고    scopus 로고
    • A component-based software environment for visualizing large macromolecular assemblies
    • Sanner, M. F. A. A component-based software environment for visualizing large macromolecular assemblies Structure 2005, 13, 447-462
    • (2005) Structure , vol.13 , pp. 447-462
    • Sanner, M.F.A.1
  • 14
    • 84867471192 scopus 로고    scopus 로고
    • Top-hits for A/H1N1 identified by virtual screening using ensemble-based docking
    • 10.1371/currents.RRN1030.
    • Nguyen, H. T.; Le, L.; Truong, T. N. Top-hits for A/H1N1 identified by virtual screening using ensemble-based docking. PLoS Curr. 2009, 10.1371/currents.RRN1030.
    • (2009) PLoS Curr.
    • Nguyen, H.T.1    Le, L.2    Truong, T.N.3
  • 15
    • 70349484061 scopus 로고    scopus 로고
    • Rational design of Tamiflu derivatives targeting at the open conformation of neuraminidase subtype 1
    • Li, Y.; Zhou, B.; Wang, R. Rational design of Tamiflu derivatives targeting at the open conformation of neuraminidase subtype 1 J. Mol. Graphics Modell. 2009, 28, 203-219
    • (2009) J. Mol. Graphics Modell. , vol.28 , pp. 203-219
    • Li, Y.1    Zhou, B.2    Wang, R.3
  • 16
    • 46149126359 scopus 로고    scopus 로고
    • Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV)
    • Mihajlovic, M. L.; Mitrasinovic, P. M. Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV) Biophys. Chem. 2008, 136, 152-158
    • (2008) Biophys. Chem. , vol.136 , pp. 152-158
    • Mihajlovic, M.L.1    Mitrasinovic, P.M.2
  • 17
    • 56449084239 scopus 로고    scopus 로고
    • Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza h6n1 wild-type neuraminidase and of the oseltamivir-resistant h274y variant
    • Garcia-Sosa, A. T.; Sild, S.; Maran, U. Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza h6n1 wild-type neuraminidase and of the oseltamivir-resistant h274y variant J. Chem. Inf. Model. 2008, 48, 2074-2080
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2074-2080
    • Garcia-Sosa, A.T.1    Sild, S.2    Maran, U.3
  • 18
    • 34548261773 scopus 로고    scopus 로고
    • Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus
    • Du, Q. S.; Wang, S. Q.; Chou, K. C. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus Biochem. Biophys. Res. Commun. 2007, 362, 525-531
    • (2007) Biochem. Biophys. Res. Commun. , vol.362 , pp. 525-531
    • Du, Q.S.1    Wang, S.Q.2    Chou, K.C.3
  • 19
    • 68149157302 scopus 로고    scopus 로고
    • Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs)
    • Mihajlovic, M. L.; Mitrasinovic, P. M. Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs) Mol. Simul. 2009, 35, 311-324
    • (2009) Mol. Simul. , vol.35 , pp. 311-324
    • Mihajlovic, M.L.1    Mitrasinovic, P.M.2
  • 20
    • 68849094171 scopus 로고    scopus 로고
    • Some novel insights into the binding of oseltamivir and zanamivir to H5N1 and N9 influenza virus neuraminidases: A homology modeling and flexible docking study
    • Mihajlovic, M. L.; Mitrasinovic, P. M. Some novel insights into the binding of oseltamivir and zanamivir to H5N1 and N9 influenza virus neuraminidases: a homology modeling and flexible docking study J. Serb. Chem. Soc. 2009, 74, 1-13
    • (2009) J. Serb. Chem. Soc. , vol.74 , pp. 1-13
    • Mihajlovic, M.L.1    Mitrasinovic, P.M.2
  • 21
    • 58649090243 scopus 로고    scopus 로고
    • On the structure-based design of novel inhibitors of H5N1 influenza A virus neuraminidase (NA)
    • Mitrasinovic, P. M. On the structure-based design of novel inhibitors of H5N1 influenza A virus neuraminidase (NA) Biophys. Chem. 2009, 140, 35-38
    • (2009) Biophys. Chem. , vol.140 , pp. 35-38
    • Mitrasinovic, P.M.1
  • 22
    • 77950832743 scopus 로고    scopus 로고
    • Advances in the structure-based design of the influenza A neuraminidase inhibitors
    • Mitrasinovic, P. M. Advances in the structure-based design of the influenza A neuraminidase inhibitors Curr. Drug Targets 2010, 11, 315-326
    • (2010) Curr. Drug Targets , vol.11 , pp. 315-326
    • Mitrasinovic, P.M.1
  • 23
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 24
    • 56449084239 scopus 로고    scopus 로고
    • Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant
    • Garcia-Sosa, A. T.; Sild, S.; Maran, U. Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant J. Chem. Inf. Model. 2008, 48, 2074-2080
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2074-2080
    • Garcia-Sosa, A.T.1    Sild, S.2    Maran, U.3
  • 26
    • 0033576654 scopus 로고    scopus 로고
    • Binding constants of neuraminidase inhibitors: An investigation of the linear interaction energy method
    • Wall, I. D.; Leach, A. R.; Salt, D. W.; Ford, M. G.; Essex, J. W. Binding constants of neuraminidase inhibitors: An investigation of the linear interaction energy method J. Med. Chem. 1999, 42, 5142-5152
    • (1999) J. Med. Chem. , vol.42 , pp. 5142-5152
    • Wall, I.D.1    Leach, A.R.2    Salt, D.W.3    Ford, M.G.4    Essex, J.W.5
  • 28
    • 73549091448 scopus 로고    scopus 로고
    • Computational design of novel, high-affinity neuraminidase inhibitors for H5N1 avian influenza virus
    • Park, J. W.; Jo, W. H. Computational design of novel, high-affinity neuraminidase inhibitors for H5N1 avian influenza virus Eur. J. Med. Chem. 2009, 45, 536-541
    • (2009) Eur. J. Med. Chem. , vol.45 , pp. 536-541
    • Park, J.W.1    Jo, W.H.2
  • 29
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases J. Chem. Phys. 1954, 22, 1420-1426
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 30
    • 33745472162 scopus 로고    scopus 로고
    • Free energy simulations of uncatalyzed DNA replication fidelity: Structure and stability of T center dot G and dTTP center dot G terminal DNA mismatches flanked by a single dangling nucleotide
    • Bren, U.; Martinek, V.; Florian, J. Free energy simulations of uncatalyzed DNA replication fidelity: Structure and stability of T center dot G and dTTP center dot G terminal DNA mismatches flanked by a single dangling nucleotide J. Phys. Chem. B 2006, 110, 10557-10566
    • (2006) J. Phys. Chem. B , vol.110 , pp. 10557-10566
    • Bren, U.1    Martinek, V.2    Florian, J.3
  • 31
    • 0026596911 scopus 로고
    • Calculation of antibody antigen interactions-microscopic and semimicroscopic evaluation of the free energies of binding of phosphorylcholine analogs to MCPC603
    • Lee, F. S.; Chu, Z. T.; Bolger, M. B.; Warshel, A. Calculation of antibody antigen interactions-microscopic and semimicroscopic evaluation of the free energies of binding of phosphorylcholine analogs to MCPC603 Protein Eng. 1992, 5, 215-228
    • (1992) Protein Eng. , vol.5 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 32
    • 77749279875 scopus 로고    scopus 로고
    • DNA duplex stability: The role of preorganized electrostatics
    • Bren, U.; Lah, J.; Bren, M.; Martinek, V.; Florian, J. DNA duplex stability: the role of preorganized electrostatics J. Phys. Chem. B 2010, 114, 2876-2885
    • (2010) J. Phys. Chem. B , vol.114 , pp. 2876-2885
    • Bren, U.1    Lah, J.2    Bren, M.3    Martinek, V.4    Florian, J.5
  • 33
    • 63449087331 scopus 로고    scopus 로고
    • Computational studies of H5N1 influenza virus resistance to oseltamivir
    • Wang, N. X.; Zheng, J. J. Computational studies of H5N1 influenza virus resistance to oseltamivir Protein Sci. 2009, 18, 707-715
    • (2009) Protein Sci. , vol.18 , pp. 707-715
    • Wang, N.X.1    Zheng, J.J.2
  • 34
    • 0346996361 scopus 로고    scopus 로고
    • Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations
    • Masukawa, K. M.; Kollman, P. A.; Kuntz, I. D. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations J. Med. Chem. 2003, 46, 5628-5637
    • (2003) J. Med. Chem. , vol.46 , pp. 5628-5637
    • Masukawa, K.M.1    Kollman, P.A.2    Kuntz, I.D.3
  • 35
    • 1842611470 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analysis of neuraminidase ligand interactions
    • Bonnet, P.; Bryce, R. A. Molecular dynamics and free energy analysis of neuraminidase ligand interactions Protein Sci. 2004, 13, 946-957
    • (2004) Protein Sci. , vol.13 , pp. 946-957
    • Bonnet, P.1    Bryce, R.A.2
  • 36
    • 57749118013 scopus 로고    scopus 로고
    • Origins of resistance conferred by the r292k neuraminidase mutation via molecular dynamics and free energy calculations
    • Chachra, R.; Rizzo, R. C. Origins of resistance conferred by the r292k neuraminidase mutation via molecular dynamics and free energy calculations J. Chem. Theory Comput. 2008, 4, 1526-1540
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1526-1540
    • Chachra, R.1    Rizzo, R.C.2
  • 37
    • 65249136476 scopus 로고    scopus 로고
    • Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: Determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir
    • Lawrenz, M.; Baron, R.; McCammon., J. A. Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: Determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir J. Chem. Theory Comput. 2008, 5, 1106-1116
    • (2008) J. Chem. Theory Comput. , vol.5 , pp. 1106-1116
    • Lawrenz, M.1    Baron, R.2    McCammon, J.A.3
  • 39
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • DOI 10.1016/S0959-440X(00)00194-9
    • Isralewitz, B.; Gao, M.; Schulten, K. Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 2001, 11, 224-230 (Pubitemid 32289426)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.2 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 40
    • 0031848099 scopus 로고    scopus 로고
    • Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
    • Lu, H.; Isralewitz, B.; Krammer, A.; Vogel, V.; Schulten, K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation Biophys. J. 1998, 75, 662-671
    • (1998) Biophys. J. , vol.75 , pp. 662-671
    • Lu, H.1    Isralewitz, B.2    Krammer, A.3    Vogel, V.4    Schulten, K.5
  • 41
    • 0030834853 scopus 로고    scopus 로고
    • Binding pathway of retinal to bacterioopsin: A prediction by molecular dynamics simulations
    • Isralewitz, B.; Izrailev, S.; Schulten, K. Binding pathway of retinal to bacterioopsin: A prediction by molecular dynamics simulations Biophys. J. 1997, 73, 2972-2979
    • (1997) Biophys. J. , vol.73 , pp. 2972-2979
    • Isralewitz, B.1    Izrailev, S.2    Schulten, K.3
  • 42
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmuller, H.; Heymann, B.; Tavan, P. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force Science 1996, 271, 997-999
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmuller, H.1    Heymann, B.2    Tavan, P.3
  • 43
    • 33749474932 scopus 로고    scopus 로고
    • Ligand-release pathways in the pheromone-binding protein of Bombyx mori
    • Garter, F.; de Groot, B. L.; Jiang, H.; Grubmuller., H. Ligand-release pathways in the pheromone-binding protein of Bombyx mori Structure. 2006, 14, 1567-1576
    • (2006) Structure. , vol.14 , pp. 1567-1576
    • Garter, F.1    De Groot, B.L.2    Jiang, H.3    Grubmuller, H.4
  • 44
    • 0041691306 scopus 로고    scopus 로고
    • How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations
    • Xu, Y.; Shen, J.; Luo, X.; Silman, I.; Sussman, J. L.; Chen, K.; Jiang, H. How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations J. Am. Chem. Soc. 2003, 125, 11340-11349
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 11340-11349
    • Xu, Y.1    Shen, J.2    Luo, X.3    Silman, I.4    Sussman, J.L.5    Chen, K.6    Jiang, H.7
  • 46
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
    • Park, S.; Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality J. Chem. Phys. 2003, 119, 3559-3566
    • (2003) J. Chem. Phys. , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 48
    • 33644938813 scopus 로고    scopus 로고
    • Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain
    • Zhang, D.; Gullingsrud, J.; McCammon, J. A. Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain J. Am. Chem. Soc. 2006, 128, 3019-3026
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 3019-3026
    • Zhang, D.1    Gullingsrud, J.2    McCammon, J.A.3
  • 49
    • 65149099238 scopus 로고    scopus 로고
    • Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations
    • Ytreberg, F. M. Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations J. Chem. Phys. 2009, 130, 164906
    • (2009) J. Chem. Phys. , vol.130 , pp. 164906
    • Ytreberg, F.M.1
  • 50
    • 33749551900 scopus 로고    scopus 로고
    • Odorant binding and conformational dynamics in the odorant-binding protein
    • Hajjar, E.; Perahia, D.; Debat, H.; Nespoulous, C.; Robert, C. H. Odorant binding and conformational dynamics in the odorant-binding protein J. Biol. Chem. 2006, 281, 29929-29937
    • (2006) J. Biol. Chem. , vol.281 , pp. 29929-29937
    • Hajjar, E.1    Perahia, D.2    Debat, H.3    Nespoulous, C.4    Robert, C.H.5
  • 51
    • 0001398008 scopus 로고    scopus 로고
    • How well does restrained electrostatic potential (RESP) model perform organic and biological molecules
    • Wang, J.; Cieplak, P.; Kollman, P. A. How well does restrained electrostatic potential (RESP) model perform organic and biological molecules J. Comput. Chem. 2000, 21, 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 54
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • DOI 10.1021/ja990935j
    • Massova, I.; Kollman, P. A. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies J. Am. Chem. Soc. 1999, 121, 8133-8143 (Pubitemid 29444447)
    • (1999) Journal of the American Chemical Society , vol.121 , Issue.36 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 55
    • 33749447306 scopus 로고    scopus 로고
    • A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides
    • Ganoth, A.; Friedman, R.; Nachliel, E.; Gutman, M. A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides Biophys. J. 2006, 91, 2436-2450
    • (2006) Biophys. J. , vol.91 , pp. 2436-2450
    • Ganoth, A.1    Friedman, R.2    Nachliel, E.3    Gutman, M.4
  • 56
    • 66249090517 scopus 로고    scopus 로고
    • Modeling the interaction between the N-terminal domain of the tumor suppressor p53 and azurin
    • Taranta, M.; Bizzarri, A. R.; Cannistraro, S. Modeling the interaction between the N-terminal domain of the tumor suppressor p53 and azurin J. Mol. Recognit. 2008, 22, 215-222
    • (2008) J. Mol. Recognit. , vol.22 , pp. 215-222
    • Taranta, M.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 57
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 61
    • 0030158429 scopus 로고    scopus 로고
    • PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
    • van Aalten, D. M. F.; Bywater, R.; Findlay, J. B. C.; Hendlich, M.; Hooft, R. W. W.; Vriend, G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules J. Comput.-Aided. Mol. Des. 1996, 10, 255-262
    • (1996) J. Comput.-Aided. Mol. Des. , vol.10 , pp. 255-262
    • Van Aalten, D.M.F.1    Bywater, R.2    Findlay, J.B.C.3    Hendlich, M.4    Hooft, R.W.W.5    Vriend, G.6
  • 63
    • 0347784245 scopus 로고
    • Quit high resolution computer models of plasma
    • Hockney, R. W.; Goel, S. P.; Eastwood, J. Quit high resolution computer models of plasma J. Comput. Phys. 1974, 14, 148-158
    • (1974) J. Comput. Phys. , vol.14 , pp. 148-158
    • Hockney, R.W.1    Goel, S.P.2    Eastwood, J.3
  • 65
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 67
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182-7190
    • (1981) J. Appl. Phys. , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 68
    • 74249086852 scopus 로고    scopus 로고
    • Biomolecules under mechanical force
    • Kumar, S.; Li, M. S. Biomolecules under mechanical force Phys. Rep. 2010, 486, 1-74
    • (2010) Phys. Rep. , vol.486 , pp. 1-74
    • Kumar, S.1    Li, M.S.2
  • 69
    • 38849169933 scopus 로고    scopus 로고
    • New force replica exchange method and protein folding pathways probed by force-clamp technique
    • 045103
    • Kouza, M.; Hu, C. K.; Li, M. S. New force replica exchange method and protein folding pathways probed by force-clamp technique J. Chem. Phys. 2008, 128 045103
    • (2008) J. Chem. Phys. , vol.128
    • Kouza, M.1    Hu, C.K.2    Li, M.S.3
  • 71
  • 72
    • 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, 12782-12788
    • (2006) J. Phys. Chem. B , vol.110 , pp. 12782-12788
    • Bren, U.1    Martinek, V.2    Florian, J.3
  • 73
    • 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, 535-540
    • (2007) Theor. Chem. Acc. , vol.117 , pp. 535-540
    • Bren, M.1    Florian, J.2    Mavri, J.3    Bren, U.4
  • 74
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp, K. A.; Honig, B. Electrostatic interactions in macromolecules: Theory and applications Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 76
    • 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, 97, 1978-1988
    • (1994) J. Phys. Chem. , vol.97 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 77
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms-lysozyme and insulin
    • Shrake, A.; Rupley, J. A. Environment and exposure to solvent of protein atoms-lysozyme and insulin J. Mol. Biol. 1973, 79, 351-371
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 78
    • 84968497764 scopus 로고
    • Conditioning of quasi-Newton methods for function minimization
    • Shanno, D. F. Conditioning of quasi-Newton methods for function minimization Math. Comput. 1970, 24, 647-656
    • (1970) Math. Comput. , vol.24 , pp. 647-656
    • Shanno, D.F.1
  • 81
    • 25844438380 scopus 로고    scopus 로고
    • Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: A cause for concern
    • Bright, R. A.; Medina, M. J.; Xu, X. Y.; Perez-Oronoz, G.; Wallis, T. R.; Davis, X. H. M.; Povinelli, L.; Cox, N. J.; Klimov, A. I. Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: A cause for concern Lancet 2005, 366, 1175-1181
    • (2005) Lancet , vol.366 , pp. 1175-1181
    • Bright, R.A.1    Medina, M.J.2    Xu, X.Y.3    Perez-Oronoz, G.4    Wallis, T.R.5    Davis, X.H.M.6    Povinelli, L.7    Cox, N.J.8    Klimov, A.I.9
  • 82
    • 70350510084 scopus 로고    scopus 로고
    • Dynamic behavior of avian influenza A virus neuraminidase subtype H5N1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues
    • Udommaneethanakit, T.; Rungrotmongkol, T.; U, U. B.; Frecer, V.; Miertus, S. Dynamic behavior of avian influenza A virus neuraminidase subtype H5N1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues J. Chem. Inf. Model. 2009, 49, 2323-2332
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2323-2332
    • Udommaneethanakit, T.1    Rungrotmongkol, T.2    B, U.U.3    Frecer, V.4    Miertus, S.5
  • 84
    • 0034801450 scopus 로고    scopus 로고
    • Comparison of efficacies of RWJ-270201, zanamivir, and oseltamivir against H5N1, H9N2, and other avian influenza viruses
    • Govorkova, E. A.; Leneva, I. A.; Goloubeva, O. G.; Bush, K.; Webster, R. G. Comparison of efficacies of RWJ-270201, zanamivir, and oseltamivir against H5N1, H9N2, and other avian influenza viruses Antimicrob. Agents Chemother. 2001, 45, 2723-2732
    • (2001) Antimicrob. Agents Chemother. , vol.45 , pp. 2723-2732
    • Govorkova, E.A.1    Leneva, I.A.2    Goloubeva, O.G.3    Bush, K.4    Webster, R.G.5
  • 85
    • 84896410360 scopus 로고    scopus 로고
    • The activity of neuraminidase inhibitor oseltamivir against all subtypes of influenza viruses
    • In;, Ed; Nova Science Publishers Inc: New York,; pp.
    • Roberts, N. A.; Govorkova, E. A. The activity of neuraminidase inhibitor oseltamivir against all subtypes of influenza viruses. In Global View of the Fight against Influenza; Mitrasinovic, P. M., Ed; Nova Science Publishers Inc: New York, 2009; pp 93 - 118.
    • (2009) Global View of the Fight Against Influenza , pp. 93-118
    • Roberts, N.A.1    Govorkova, E.A.2    Mitrasinovic, P.M.3
  • 86
    • 48649107959 scopus 로고    scopus 로고
    • A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation
    • Liu, X.; Wang, X.; Jiang, H. A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation J. Biochem. Biophys. Methods 2008, 70, 857-864
    • (2008) J. Biochem. Biophys. Methods , vol.70 , pp. 857-864
    • Liu, X.1    Wang, X.2    Jiang, H.3
  • 87
    • 58149526293 scopus 로고    scopus 로고
    • A steered molecular dynamics method with adaptive direction adjustments
    • Yang, K.; Liu, X.; Wang, X.; Jiang, H. A steered molecular dynamics method with adaptive direction adjustments Biochem. Biophys. Res. Commun. 2009, 379, 494-498
    • (2009) Biochem. Biophys. Res. Commun. , vol.379 , pp. 494-498
    • Yang, K.1    Liu, X.2    Wang, X.3    Jiang, H.4
  • 88
    • 0033917135 scopus 로고    scopus 로고
    • The key event in force-induced unfolding of titin's immunoglobulin domain
    • Lu, H.; Schulten, K. The key event in force-induced unfolding of titin's immunoglobulin domain Biophys. J. 2000, 79, 51-65
    • (2000) Biophys. J. , vol.79 , pp. 51-65
    • Lu, H.1    Schulten, K.2
  • 89
    • 77952844866 scopus 로고    scopus 로고
    • Single-molecule pulling simulations can discern active from inactive enzyme inhibitors
    • Colizzi, F.; Perozzo, R.; Scapozza, L.; Recanatini, M.; Cavalli, A. Single-molecule pulling simulations can discern active from inactive enzyme inhibitors J. Am. Chem. Soc. 2010, 132, 7361-7371
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 7361-7371
    • Colizzi, F.1    Perozzo, R.2    Scapozza, L.3    Recanatini, M.4    Cavalli, A.5
  • 90
    • 77954228177 scopus 로고    scopus 로고
    • Drug discovery pulled from a proteins's embrace
    • Jorgensen, W. L. Drug discovery pulled from a proteins's embrace Nature 2010, 466, 42-43
    • (2010) Nature , vol.466 , pp. 42-43
    • Jorgensen, W.L.1


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