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Volumn 53, Issue 7, 2013, Pages 1700-1713

Water network perturbation in ligand binding: Adenosine A2A antagonists as a case study

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); FORECASTING; FREE ENERGY; LEARNING SYSTEMS; LIGANDS; MOLECULES; MONTE CARLO METHODS;

EID: 84880564425     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4001458     Document Type: Article
Times cited : (110)

References (93)
  • 1
    • 38849196324 scopus 로고    scopus 로고
    • Water as an active constituent in cell biology
    • Ball, P. Water as an active constituent in cell biology Chem. Rev. 2008, 108 (1) 74-108
    • (2008) Chem. Rev. , vol.108 , Issue.1 , pp. 74-108
    • Ball, P.1
  • 4
  • 5
    • 34249079980 scopus 로고    scopus 로고
    • Molecular modeling of hydration in drug design
    • Mancera, R. L. Molecular modeling of hydration in drug design Curr. Opin. Drug Discov. Devel. 2007, 10 (3) 275-280
    • (2007) Curr. Opin. Drug Discov. Devel. , vol.10 , Issue.3 , pp. 275-280
    • Mancera, R.L.1
  • 6
    • 78650667884 scopus 로고    scopus 로고
    • Accounting for water molecules in drug design
    • Wong, S. E.; Lightstone, F. C. Accounting for water molecules in drug design Expert. Opin. Drug Discov. 2011, 6 (1) 65-74
    • (2011) Expert. Opin. Drug Discov. , vol.6 , Issue.1 , pp. 65-74
    • Wong, S.E.1    Lightstone, F.C.2
  • 8
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28 (7) 849-857
    • (1985) J. Med. Chem. , vol.28 , Issue.7 , pp. 849-857
    • Goodford, P.J.1
  • 9
    • 0029812557 scopus 로고    scopus 로고
    • Simulated Annealing of Chemical-Potential-A General Procedure for Locating Bound Waters-Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA
    • Guarnieri, F.; Mezei, M. Simulated Annealing of Chemical-Potential-A General Procedure for Locating Bound Waters-Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA J. Am. Chem. Soc. 1996, 118 (35) 8493-8494
    • (1996) J. Am. Chem. Soc. , vol.118 , Issue.35 , pp. 8493-8494
    • Guarnieri, F.1    Mezei, M.2
  • 10
    • 70349683018 scopus 로고    scopus 로고
    • Prediction of the water content in protein binding sites
    • Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. Prediction of the water content in protein binding sites J. Phys. Chem. B 2009, 113 (40) 13337-13346
    • (2009) J. Phys. Chem. B , vol.113 , Issue.40 , pp. 13337-13346
    • Michel, J.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 11
    • 33847655150 scopus 로고    scopus 로고
    • Classification of water molecules in protein binding sites
    • Barillari, C.; Taylor, J.; Viner, R.; Essex, J. W. Classification of water molecules in protein binding sites J. Am. Chem. Soc. 2007, 129 (9) 2577-2587
    • (2007) J. Am. Chem. Soc. , vol.129 , Issue.9 , pp. 2577-2587
    • Barillari, C.1    Taylor, J.2    Viner, R.3    Essex, J.W.4
  • 12
    • 33847010225 scopus 로고    scopus 로고
    • Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation
    • Imai, T.; Hiraoka, R.; Kovalenko, A.; Hirata, F. Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation Proteins 2007, 66 (4) 804-813
    • (2007) Proteins , vol.66 , Issue.4 , pp. 804-813
    • Imai, T.1    Hiraoka, R.2    Kovalenko, A.3    Hirata, F.4
  • 13
    • 80052010268 scopus 로고    scopus 로고
    • AcquaAlta: A directional approach to the solvation of ligand-protein complexes
    • Rossato, G.; Ernst, B.; Vedani, A.; Smiesko, M. AcquaAlta: a directional approach to the solvation of ligand-protein complexes J. Chem. Inf. Model. 2011, 51 (8) 1867-1881
    • (2011) J. Chem. Inf. Model. , vol.51 , Issue.8 , pp. 1867-1881
    • Rossato, G.1    Ernst, B.2    Vedani, A.3    Smiesko, M.4
  • 14
    • 84857748866 scopus 로고    scopus 로고
    • Rapid and accurate prediction and scoring of water molecules in protein binding sites
    • Ross, G. A.; Morris, G. M.; Biggin, P. C. Rapid and accurate prediction and scoring of water molecules in protein binding sites PLoS. One. 2012, 7 (3) e32036
    • (2012) PLoS. One. , vol.7 , Issue.3 , pp. 32036
    • Ross, G.A.1    Morris, G.M.2    Biggin, P.C.3
  • 15
    • 40949163431 scopus 로고    scopus 로고
    • Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
    • Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding J. Am. Chem. Soc. 2008, 130 (9) 2817-2831
    • (2008) J. Am. Chem. Soc. , vol.130 , Issue.9 , pp. 2817-2831
    • Abel, R.1    Young, T.2    Farid, R.3    Berne, B.J.4    Friesner, R.A.5
  • 16
    • 79957585828 scopus 로고    scopus 로고
    • Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases
    • Abel, R.; Salam, N. K.; Shelley, J.; Farid, R.; Friesner, R. A.; Sherman, W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases ChemMedChem. 2011, 6 (6) 1049-1066
    • (2011) ChemMedChem. , vol.6 , Issue.6 , pp. 1049-1066
    • Abel, R.1    Salam, N.K.2    Shelley, J.3    Farid, R.4    Friesner, R.A.5    Sherman, W.6
  • 17
    • 77951997162 scopus 로고    scopus 로고
    • Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations
    • Guimaraes, C. R.; Mathiowetz, A. M. Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations J. Chem. Inf. Model. 2010, 50 (4) 547-559
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.4 , pp. 547-559
    • Guimaraes, C.R.1    Mathiowetz, A.M.2
  • 18
    • 77955869797 scopus 로고    scopus 로고
    • Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor
    • Higgs, C.; Beuming, T.; Sherman, W. Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor ACS Med. Chem. Lett. 2010, 1 (4) 160-164
    • (2010) ACS Med. Chem. Lett. , vol.1 , Issue.4 , pp. 160-164
    • Higgs, C.1    Beuming, T.2    Sherman, W.3
  • 20
    • 84860505658 scopus 로고    scopus 로고
    • New insights from structural biology into the druggability of G protein-coupled receptors
    • Mason, J. S.; Bortolato, A.; Congreve, M.; Marshall, F. H. New insights from structural biology into the druggability of G protein-coupled receptors Trends Pharmacol. Sci. 2012, 33 (5) 249-260
    • (2012) Trends Pharmacol. Sci. , vol.33 , Issue.5 , pp. 249-260
    • Mason, J.S.1    Bortolato, A.2    Congreve, M.3    Marshall, F.H.4
  • 21
    • 77955810437 scopus 로고    scopus 로고
    • New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor-like repeat A docking site using WaterMap
    • Pearlstein, R. A.; Hu, Q. Y.; Zhou, J.; Yowe, D.; Levell, J.; Dale, B.; Kaushik, V. K.; Daniels, D.; Hanrahan, S.; Sherman, W.; Abel, R. New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap Proteins 2010, 78 (12) 2571-2586
    • (2010) Proteins , vol.78 , Issue.12 , pp. 2571-2586
    • Pearlstein, R.A.1    Hu, Q.Y.2    Zhou, J.3    Yowe, D.4    Levell, J.5    Dale, B.6    Kaushik, V.K.7    Daniels, D.8    Hanrahan, S.9    Sherman, W.10    Abel, R.11
  • 22
    • 84865212063 scopus 로고    scopus 로고
    • Docking performance of the glide program as evaluated on the Astex and DUD datasets: A complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide
    • Repasky, M. P.; Murphy, R. B.; Banks, J. L.; Greenwood, J. R.; Tubert-Brohman, I.; Bhat, S.; Friesner, R. A. Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide J. Comput. Aided Mol. Des. 2012, 26 (6) 787-799
    • (2012) J. Comput. Aided Mol. Des. , vol.26 , Issue.6 , pp. 787-799
    • Repasky, M.P.1    Murphy, R.B.2    Banks, J.L.3    Greenwood, J.R.4    Tubert-Brohman, I.5    Bhat, S.6    Friesner, R.A.7
  • 23
    • 82355160789 scopus 로고    scopus 로고
    • A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease
    • Wallnoefer, H. G.; Liedl, K. R.; Fox, T. A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease J. Chem. Inf. Model. 2011, 51 (11) 2860-2867
    • (2011) J. Chem. Inf. Model. , vol.51 , Issue.11 , pp. 2860-2867
    • Wallnoefer, H.G.1    Liedl, K.R.2    Fox, T.3
  • 24
    • 79952161696 scopus 로고    scopus 로고
    • Ligand binding to protein-binding pockets with wet and dry regions
    • Wang, L.; Berne, B. J.; Friesner, R. A. Ligand binding to protein-binding pockets with wet and dry regions Proc. Natl. Acad. Sci. U.S.A. 2011, 108 (4) 1326-1330
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , Issue.4 , pp. 1326-1330
    • Wang, L.1    Berne, B.J.2    Friesner, R.A.3
  • 25
    • 84861801340 scopus 로고    scopus 로고
    • Placevent: An algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase
    • Sindhikara, D. J.; Yoshida, N.; Hirata, F. Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase J. Comput. Chem. 2012, 33 (18) 1536-1543
    • (2012) J. Comput. Chem. , vol.33 , Issue.18 , pp. 1536-1543
    • Sindhikara, D.J.1    Yoshida, N.2    Hirata, F.3
  • 26
    • 84863970196 scopus 로고    scopus 로고
    • Individual degrees of freedom and the solvation properties of water
    • Bren, U.; Janezic, D. Individual degrees of freedom and the solvation properties of water J. Chem. Phys. 2012, 137 (2) 024108
    • (2012) J. Chem. Phys. , vol.137 , Issue.2 , pp. 024108
    • Bren, U.1    Janezic, D.2
  • 27
    • 84882868265 scopus 로고    scopus 로고
    • Contributions of water transfer energy to protein-ligand association and dissociation barriers: WaterMap analysis of a series of p38alpha MAP kinase inhibitors
    • 10.1002/prot.24276
    • Pearlstein, R. A.; Sherman, W.; Abel, R. Contributions of water transfer energy to protein-ligand association and dissociation barriers: WaterMap analysis of a series of p38alpha MAP kinase inhibitors Proteins 2013, 10.1002/prot.24276
    • (2013) Proteins
    • Pearlstein, R.A.1    Sherman, W.2    Abel, R.3
  • 30
    • 33846302070 scopus 로고    scopus 로고
    • The role of internal water molecules in the structure and function of the rhodopsin family of G protein-coupled receptors
    • Pardo, L.; Deupi, X.; Dolker, N.; Lopez-Rodriguez, M. L.; Campillo, M. The role of internal water molecules in the structure and function of the rhodopsin family of G protein-coupled receptors Chembiochem. 2007, 8 (1) 19-24
    • (2007) Chembiochem. , vol.8 , Issue.1 , pp. 19-24
    • Pardo, L.1    Deupi, X.2    Dolker, N.3    Lopez-Rodriguez, M.L.4    Campillo, M.5
  • 31
    • 70149112575 scopus 로고    scopus 로고
    • Structural waters define a functional channel mediating activation of the GPCR, rhodopsin
    • Angel, T. E.; Gupta, S.; Jastrzebska, B.; Palczewski, K.; Chance, M. R. Structural waters define a functional channel mediating activation of the GPCR, rhodopsin Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (34) 14367-14372
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , Issue.34 , pp. 14367-14372
    • Angel, T.E.1    Gupta, S.2    Jastrzebska, B.3    Palczewski, K.4    Chance, M.R.5
  • 32
    • 79956305477 scopus 로고    scopus 로고
    • Role of bulk water in hydrolysis of the rhodopsin chromophore
    • Jastrzebska, B.; Palczewski, K.; Golczak, M. Role of bulk water in hydrolysis of the rhodopsin chromophore J. Biol. Chem. 2011, 286 (21) 18930-18937
    • (2011) J. Biol. Chem. , vol.286 , Issue.21 , pp. 18930-18937
    • Jastrzebska, B.1    Palczewski, K.2    Golczak, M.3
  • 33
    • 79960176452 scopus 로고    scopus 로고
    • Progress in structure based drug design for g protein-coupled receptors
    • Congreve, M.; Langmead, C. J.; Mason, J. S.; Marshall, F. H. Progress in structure based drug design for g protein-coupled receptors J. Med. Chem. 2011, 54 (13) 4283-4311
    • (2011) J. Med. Chem. , vol.54 , Issue.13 , pp. 4283-4311
    • Congreve, M.1    Langmead, C.J.2    Mason, J.S.3    Marshall, F.H.4
  • 34
    • 42149181885 scopus 로고    scopus 로고
    • Structural diversity of G protein-coupled receptors and significance for drug discovery
    • Lagerstrom, M. C.; Schioth, H. B. Structural diversity of G protein-coupled receptors and significance for drug discovery Nat. Rev. Drug Discov. 2008, 7 (4) 339-357
    • (2008) Nat. Rev. Drug Discov. , vol.7 , Issue.4 , pp. 339-357
    • Lagerstrom, M.C.1    Schioth, H.B.2
  • 35
    • 51049101334 scopus 로고    scopus 로고
    • Adenosine receptors: Therapeutic aspects for inflammatory and immune diseases
    • Hasko, G.; Linden, J.; Cronstein, B.; Pacher, P. Adenosine receptors: therapeutic aspects for inflammatory and immune diseases Nat. Rev. Drug Discov. 2008, 7 (9) 759-770
    • (2008) Nat. Rev. Drug Discov. , vol.7 , Issue.9 , pp. 759-770
    • Hasko, G.1    Linden, J.2    Cronstein, B.3    Pacher, P.4
  • 36
    • 33644770260 scopus 로고    scopus 로고
    • Adenosine receptors as therapeutic targets
    • Jacobson, K. A.; Gao, Z. G. Adenosine receptors as therapeutic targets Nat. Rev. Drug Discov. 2006, 5 (3) 247-264
    • (2006) Nat. Rev. Drug Discov. , vol.5 , Issue.3 , pp. 247-264
    • Jacobson, K.A.1    Gao, Z.G.2
  • 37
    • 79954503213 scopus 로고    scopus 로고
    • Adenosine and related drugs in brain diseases: Present and future in clinical trials
    • Lopes, L. V.; Sebastiao, A. M.; Ribeiro, J. A. Adenosine and related drugs in brain diseases: present and future in clinical trials Curr. Top. Med. Chem. 2011, 11 (8) 1087-1101
    • (2011) Curr. Top. Med. Chem. , vol.11 , Issue.8 , pp. 1087-1101
    • Lopes, L.V.1    Sebastiao, A.M.2    Ribeiro, J.A.3
  • 38
    • 79951720949 scopus 로고    scopus 로고
    • Preladenant in patients with Parkinson′s disease and motor fluctuations: A phase 2, double-blind, randomised trial
    • Hauser, R. A.; Cantillon, M.; Pourcher, E.; Micheli, F.; Mok, V.; Onofrj, M.; Huyck, S.; Wolski, K. Preladenant in patients with Parkinson′s disease and motor fluctuations: a phase 2, double-blind, randomised trial Lancet Neurol. 2011, 10 (3) 221-229
    • (2011) Lancet Neurol. , vol.10 , Issue.3 , pp. 221-229
    • Hauser, R.A.1    Cantillon, M.2    Pourcher, E.3    Micheli, F.4    Mok, V.5    Onofrj, M.6    Huyck, S.7    Wolski, K.8
  • 43
    • 79956124396 scopus 로고    scopus 로고
    • Thermostabilisation of an agonist-bound conformation of the human adenosine A(2A) receptor
    • Lebon, G.; Bennett, K.; Jazayeri, A.; Tate, C. G. Thermostabilisation of an agonist-bound conformation of the human adenosine A(2A) receptor J. Mol. Biol. 2011, 409 (3) 298-310
    • (2011) J. Mol. Biol. , vol.409 , Issue.3 , pp. 298-310
    • Lebon, G.1    Bennett, K.2    Jazayeri, A.3    Tate, C.G.4
  • 45
    • 79959564813 scopus 로고    scopus 로고
    • Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation
    • Lebon, G.; Warne, T.; Edwards, P. C.; Bennett, K.; Langmead, C. J.; Leslie, A. G.; Tate, C. G. Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation Nature 2011, 474 (7352) 521-525
    • (2011) Nature , vol.474 , Issue.7352 , pp. 521-525
    • Lebon, G.1    Warne, T.2    Edwards, P.C.3    Bennett, K.4    Langmead, C.J.5    Leslie, A.G.6    Tate, C.G.7
  • 48
    • 84880524287 scopus 로고    scopus 로고
    • version 1. 0; Openeye Scientific Software: Santa Fe, NM
    • SZMAP, version 1. 0; Openeye Scientific Software: Santa Fe, NM, 2011.
    • (2011) SZMAP
  • 49
    • 0001636185 scopus 로고
    • Chemical potential of hard-sphere fluids by Monte Carlo methods
    • Adams, D. J. Chemical potential of hard-sphere fluids by Monte Carlo methods Mol. Phys. 1974, 28 (5) 1241-1252
    • (1974) Mol. Phys. , vol.28 , Issue.5 , pp. 1241-1252
    • Adams, D.J.1
  • 51
    • 34247263219 scopus 로고    scopus 로고
    • A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): Theory and application
    • Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J. S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application J. Chem. Inf. Model. 2007, 47 (2) 279-294
    • (2007) J. Chem. Inf. Model. , vol.47 , Issue.2 , pp. 279-294
    • Baroni, M.1    Cruciani, G.2    Sciabola, S.3    Perruccio, F.4    Mason, J.S.5
  • 52
    • 44049103958 scopus 로고    scopus 로고
    • Residence time of receptor-ligand complexes and its effect on biological function
    • Tummino, P. J.; Copeland, R. A. Residence time of receptor-ligand complexes and its effect on biological function Biochemistry 2008, 47 (20) 5481-5492
    • (2008) Biochemistry , vol.47 , Issue.20 , pp. 5481-5492
    • Tummino, P.J.1    Copeland, R.A.2
  • 53
    • 33748325882 scopus 로고    scopus 로고
    • Drug-target residence time and its implications for lead optimization
    • Copeland, R. A.; Pompliano, D. L.; Meek, T. D. Drug-target residence time and its implications for lead optimization Nat. Rev. Drug Discov. 2006, 5 (9) 730-739
    • (2006) Nat. Rev. Drug Discov. , vol.5 , Issue.9 , pp. 730-739
    • Copeland, R.A.1    Pompliano, D.L.2    Meek, T.D.3
  • 54
    • 84879925936 scopus 로고    scopus 로고
    • Molecular determinants of drug-receptor binding kinetics
    • 10.1016/j.drudis.2013.02.007
    • Pan, A. C.; Borhani, D. W.; Dror, R. O.; Shaw, D. E. Molecular determinants of drug-receptor binding kinetics Drug Discov. Today 2013, 10.1016/j.drudis.2013.02.007
    • (2013) Drug Discov. Today
    • Pan, A.C.1    Borhani, D.W.2    Dror, R.O.3    Shaw, D.E.4
  • 55
    • 80052462704 scopus 로고    scopus 로고
    • Conformational adaptation in drug-target interactions and residence time
    • Copeland, R. A. Conformational adaptation in drug-target interactions and residence time Future. Med. Chem. 2011, 3 (12) 1491-1501
    • (2011) Future. Med. Chem. , vol.3 , Issue.12 , pp. 1491-1501
    • Copeland, R.A.1
  • 56
    • 77950197835 scopus 로고    scopus 로고
    • The dynamics of drug-target interactions: Drug-target residence time and its impact on efficacy and safety
    • Copeland, R. A. The dynamics of drug-target interactions: drug-target residence time and its impact on efficacy and safety Expert. Opin. Drug Discov. 2010, 5 (4) 305-310
    • (2010) Expert. Opin. Drug Discov. , vol.5 , Issue.4 , pp. 305-310
    • Copeland, R.A.1
  • 58
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman, L. Random Forests Mach. Learn. 2001, 45 (1) 5-32
    • (2001) Mach. Learn. , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 59
    • 28944450149 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions using random decision forest framework
    • Chen, X. W.; Liu, M. Prediction of protein-protein interactions using random decision forest framework Bioinformatics 2005, 21 (24) 4394-4400
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4394-4400
    • Chen, X.W.1    Liu, M.2
  • 60
    • 75749126524 scopus 로고    scopus 로고
    • Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening
    • Sato, T.; Honma, T.; Yokoyama, S. Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening J. Chem. Inf. Model. 2010, 50 (1) 170-185
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.1 , pp. 170-185
    • Sato, T.1    Honma, T.2    Yokoyama, S.3
  • 61
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
    • Ballester, P. J.; Mitchell, J. B. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking Bioinformatics 2010, 26 (9) 1169-1175
    • (2010) Bioinformatics , vol.26 , Issue.9 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.2
  • 62
    • 69549135452 scopus 로고    scopus 로고
    • Fragment-based computation of binding free energies by systematic sampling
    • Clark, M.; Meshkat, S.; Talbot, G. T.; Carnevali, P.; Wiseman, J. S. Fragment-based computation of binding free energies by systematic sampling J. Chem. Inf. Model. 2009, 49 (8) 1901-1913
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.8 , pp. 1901-1913
    • Clark, M.1    Meshkat, S.2    Talbot, G.T.3    Carnevali, P.4    Wiseman, J.S.5
  • 63
    • 77957055780 scopus 로고
    • Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors
    • Ballesteros, J. A.; Weinstein, H. Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors Methods Neurosci. 1995, 25, 366-428
    • (1995) Methods Neurosci. , vol.25 , pp. 366-428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 64
    • 83055179348 scopus 로고    scopus 로고
    • Shielded hydrogen bonds as structural determinants of binding kinetics: Application in drug design
    • Schmidtke, P.; Luque, F. J.; Murray, J. B.; Barril, X. Shielded hydrogen bonds as structural determinants of binding kinetics: application in drug design J. Am. Chem. Soc. 2011, 133 (46) 18903-18910
    • (2011) J. Am. Chem. Soc. , vol.133 , Issue.46 , pp. 18903-18910
    • Schmidtke, P.1    Luque, F.J.2    Murray, J.B.3    Barril, X.4
  • 66
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke, H.; Case, D. A. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf J. Comput. Chem. 2004, 25 (2) 238-250
    • (2004) J. Comput. Chem. , vol.25 , Issue.2 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 67
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design Protein Eng. 1994, 7 (3) 385-391
    • (1994) Protein Eng. , vol.7 , Issue.3 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 68
    • 84862884578 scopus 로고    scopus 로고
    • Cytochrome P450 3A4 inhibition by ketoconazole: Tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations
    • Bren, U.; Oostenbrink, C. Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations J. Chem. Inf. Model. 2012, 52 (6) 1573-1582
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.6 , pp. 1573-1582
    • Bren, U.1    Oostenbrink, C.2
  • 69
    • 34247236710 scopus 로고    scopus 로고
    • In silico binding free energy predictability by using the linear interaction energy (LIE) method: Bromobenzimidazole CK2 inhibitors as a case study
    • Bortolato, A.; Moro, S. In silico binding free energy predictability by using the linear interaction energy (LIE) method: bromobenzimidazole CK2 inhibitors as a case study J. Chem. Inf. Model. 2007, 47 (2) 572-582
    • (2007) J. Chem. Inf. Model. , vol.47 , Issue.2 , pp. 572-582
    • Bortolato, A.1    Moro, S.2
  • 70
    • 0026596911 scopus 로고
    • Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
    • Lee, F. S.; Chu, Z. T.; Bolger, M. B.; Warshel, A. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603 Protein Eng. 1992, 5 (3) 215-228
    • (1992) Protein Eng. , vol.5 , Issue.3 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 71
    • 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 (8) 2876-2885
    • (2010) J. Phys. Chem. B , vol.114 , Issue.8 , pp. 2876-2885
    • Bren, U.1    Lah, J.2    Bren, M.3    Martinek, V.4    Florian, J.5
  • 72
    • 33746872935 scopus 로고    scopus 로고
    • Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring
    • Lyne, P. D.; Lamb, M. L.; Saeh, J. C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring J. Med. Chem. 2006, 49 (16) 4805-4808
    • (2006) J. Med. Chem. , vol.49 , Issue.16 , pp. 4805-4808
    • Lyne, P.D.1    Lamb, M.L.2    Saeh, J.C.3
  • 74
    • 33646855259 scopus 로고    scopus 로고
    • version 8. 5; Accelrys: San Diego, CA
    • Pipeline Pilot, version 8. 5; Accelrys: San Diego, CA, 2011.
    • (2011) Pipeline Pilot
  • 75
    • 0031022887 scopus 로고    scopus 로고
    • Additivity principles in biochemistry
    • Dill, K. A. Additivity principles in biochemistry J. Biol. Chem. 1997, 272 (2) 701-704
    • (1997) J. Biol. Chem. , vol.272 , Issue.2 , pp. 701-704
    • Dill, K.A.1
  • 76
    • 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
  • 77
    • 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
  • 78
    • 84880541068 scopus 로고    scopus 로고
    • version 1. 5; Schrödinger: New York
    • Canvas, version 1. 5; Schrödinger: New York, 2012.
    • (2012) Canvas
  • 79
    • 37249023309 scopus 로고    scopus 로고
    • New and original pKa prediction method using grid molecular interaction fields
    • Milletti, F.; Storchi, L.; Sforna, G.; Cruciani, G. New and original pKa prediction method using grid molecular interaction fields J. Chem. Inf. Model. 2007, 47 (6) 2172-2181
    • (2007) J. Chem. Inf. Model. , vol.47 , Issue.6 , pp. 2172-2181
    • Milletti, F.1    Storchi, L.2    Sforna, G.3    Cruciani, G.4
  • 80
    • 61949390938 scopus 로고    scopus 로고
    • Tautomer enumeration and stability prediction for virtual screening on large chemical databases
    • Milletti, F.; Storchi, L.; Sforna, G.; Cross, S.; Cruciani, G. Tautomer enumeration and stability prediction for virtual screening on large chemical databases J. Chem. Inf. Model. 2009, 49 (1) 68-75
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.1 , pp. 68-75
    • Milletti, F.1    Storchi, L.2    Sforna, G.3    Cross, S.4    Cruciani, G.5
  • 81
    • 84880523780 scopus 로고    scopus 로고
    • version 2. 1; Molecular Networks: Erlanger, Germany.
    • Corina, version 2. 1; Molecular Networks: Erlanger, Germany, 2011.
    • (2011) Corina
  • 83
    • 84880548933 scopus 로고    scopus 로고
    • version 5. 7; Schrödinger: New York
    • Glide, version 5. 7; Schrödinger: New York, 2011.
    • (2011) Glide
  • 84
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend, G. WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 1990, 8 (1) 52-6-29
    • (1990) J. Mol. Graph. , vol.8 , Issue.1 , pp. 52-629
    • Vriend, G.1
  • 86
    • 0001041959 scopus 로고    scopus 로고
    • Fast, efficient generation of high quality atomic Charges. AM1-BCC model: I. Method
    • Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high quality atomic Charges. AM1-BCC model: I. Method J. Comput. Chem. 2000, 21 (2) 132-146
    • (2000) J. Comput. Chem. , vol.21 , Issue.2 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 88
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21 (12) 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 89
    • 7044249333 scopus 로고    scopus 로고
    • Grand canonical Monte Carlo simulations of water in protein environments
    • Woo, H. J.; Dinner, A. R.; Roux, B. Grand canonical Monte Carlo simulations of water in protein environments J. Chem. Phys. 2004, 121, 6392
    • (2004) J. Chem. Phys. , vol.121 , pp. 6392
    • Woo, H.J.1    Dinner, A.R.2    Roux, B.3
  • 91
    • 84880562949 scopus 로고    scopus 로고
    • version 9.2; Schrödinger: New York
    • Maestro, version 9.2; Schrödinger: New York, 2011.
    • (2011) Maestro
  • 92
    • 37249062877 scopus 로고    scopus 로고
    • version 3.1; Accelrys: San Diego, CA
    • Discovery Studio, version 3.1; Accelrys: San Diego, CA, 2011.
    • (2011) Discovery Studio
  • 93
    • 84880529774 scopus 로고    scopus 로고
    • version 3.0; Schrödinger: New York
    • Prime, version 3.0; Schrödinger: New York, 2011.
    • (2011) Prime


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