메뉴 건너뛰기




Volumn 11, Issue 2, 2011, Pages 171-178

Accommodating protein flexibility for structure-based drug design

Author keywords

Docking; Drug design; Molecular dynamics; Protein flexibility; Relaxed complex scheme

Indexed keywords

ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DRUG DESIGN; DRUG PROTEIN BINDING; DRUG STRUCTURE; EVOLUTIONARY ALGORITHM; GENETIC ALGORITHM; LINEAR INTERACTION ENERGY; METHODOLOGY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MONTE CARLO METHOD; NORMAL DISTRIBUTION; PARTICLE SWARM ALGORITHM; POISSON BOLTZMANN SURFACE AREA; PROBABILITY; PROTEIN CONFORMATION; SCORING SYSTEM;

EID: 78649893079     PISSN: 15680266     EISSN: None     Source Type: Journal    
DOI: 10.2174/156802611794863580     Document Type: Article
Times cited : (58)

References (86)
  • 2
    • 67249096746 scopus 로고    scopus 로고
    • Functional and shunt states of bacteriorhodopsin resolvedby 250 GHz dynamic nuclear polarization-enhanced solidstateNMR
    • Bajaj, V. S.; Mak-Jurkauskas, M. L.; Belenky, M.; Herzfeld, J.; Griffin, R. G. Functional and shunt states of bacteriorhodopsin resolvedby 250 GHz dynamic nuclear polarization-enhanced solidstateNMR. Proc. Natl. Acad. Sci. USA, 2009, 106, 9244-9249.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 9244-9249
    • Bajaj, V.S.1    Mak-Jurkauskas, M.L.2    Belenky, M.3    Herzfeld, J.4    Griffin, R.G.5
  • 4
    • 67650359927 scopus 로고    scopus 로고
    • Force field biasin protein folding simulations
    • Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Force field biasin protein folding simulations. Biophys. J., 2009, 96, 3772-3780.
    • (2009) Biophys. J. , vol.96 , pp. 3772-3780
    • Freddolino, P.L.1    Park, S.2    Roux, B.3    Schulten, K.4
  • 5
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple amber force fields and developmentof improved protein backbone parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple amber force fields and developmentof improved protein backbone parameters. Proteins, 2006, 65, 712-725.
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 6
    • 64649101249 scopus 로고    scopus 로고
    • Longtimescalemolecular dynamics simulations of protein structure and function
    • Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Longtimescalemolecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol., 2009, 19, 120-127.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 120-127
    • Klepeis, J.L.1    Lindorff-Larsen, K.2    Dror, R.O.3    Shaw, D.E.4
  • 9
    • 33747200808 scopus 로고    scopus 로고
    • Combining docking and molecular dynamic simulations in drug design
    • Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Combining docking and molecular dynamic simulations in drug design. Med. Res. Rev., 2006, 26, 531-568.
    • (2006) Med. Res. Rev. , vol.26 , pp. 531-568
    • Alonso, H.1    Bliznyuk, A.A.2    Gready, J.E.3
  • 10
    • 38149088192 scopus 로고    scopus 로고
    • Flexible ligand-flexible protein docking in proteinkinase systems
    • Wong, C. F. Flexible ligand-flexible protein docking in proteinkinase systems, Biochim. Biophys. Acta Protein Proteomics, 2008, 1784, 244-251.
    • (2008) Biochim. Biophys. Acta Protein Proteomics , vol.1784 , pp. 244-251
    • Wong, C.F.1
  • 11
    • 63149162777 scopus 로고    scopus 로고
    • Managing protein flexibilityin docking and its applications
    • B-Rao, C.; Subramanian, J.; Sharma, S. D. Managing protein flexibilityin docking and its applications. Drug Discov. Today, 2009, 14, 394-400.
    • (2009) Drug Discov. Today , vol.14 , pp. 394-400
    • Rao, B.C.1    Subramanian, J.2    Sharma, S.D.3
  • 12
    • 67349261359 scopus 로고    scopus 로고
    • Effects of protein conformation in docking: Improvedpose prediction through protein pocket adaptation
    • Jain, A. N. Effects of protein conformation in docking: improvedpose prediction through protein pocket adaptation. J. Comput.-Aided. Mol. Des., 2009, 23, 355-374.
    • (2009) J. Comput.-Aided. Mol. Des. , vol.23 , pp. 355-374
    • Jain, A.N.1
  • 14
    • 37849031192 scopus 로고    scopus 로고
    • Sampling of the native conformational ensemble of myoglobinvia structures in different crystalline environments
    • Kondrashov, D. A.; Zhang, W.; Aranda, R.; Stec, B.; Phillips, G.N. Sampling of the native conformational ensemble of myoglobinvia structures in different crystalline environments. Proteins, 2008, 70, 353-362.
    • (2008) Proteins , vol.70 , pp. 353-362
    • Kondrashov, D.A.1    Zhang, W.2    Aranda, R.3    Stec, B.4    Phillips, G.N.5
  • 15
    • 33748758728 scopus 로고    scopus 로고
    • Expect the unexpected or caveat for drug designers: Multiplestructure determinations using aldose reductase crystalstreated under varying soaking and co-crystallisation conditions
    • Steuber, H.; Zentgraf, M.; Gerlach, C.; Sotriffer, C. A.; Heine, A.; Klebe, G. Expect the unexpected or caveat for drug designers: Multiplestructure determinations using aldose reductase crystalstreated under varying soaking and co-crystallisation conditions. J.Mol. Biol., 2006, 363, 174-187.
    • (2006) J.Mol. Biol. , vol.363 , pp. 174-187
    • Steuber, H.1    Zentgraf, M.2    Gerlach, C.3    Sotriffer, C.A.4    Heine, A.5    Klebe, G.6
  • 16
    • 72249105167 scopus 로고    scopus 로고
    • Solution and crystal molecular dynamicssimulation study of m4-cyanovirin-n mutants complexedwith di-mannose
    • Vorontsov, II.; Miyashita, O. Solution and crystal molecular dynamicssimulation study of m4-cyanovirin-n mutants complexedwith di-mannose. Biophys. J., 2009, 97, 2532-2540.
    • (2009) Biophys. J. , vol.97 , pp. 2532-2540
    • Vorontsov, I.I.1    Miyashita, O.2
  • 17
    • 70349683018 scopus 로고    scopus 로고
    • Prediction of thewater content in protein binding sites
    • Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. Prediction of thewater content in protein binding sites. J. Phys. Chem. B, 2009, 113, 13337-13346.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 13337-13346
    • Michel, J.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 18
    • 33750014560 scopus 로고    scopus 로고
    • Solvated docking: Introducing waterinto the modelling of biomolecular complexes
    • van Dijk, A. D. J.; Bonvin, A. Solvated docking: introducing waterinto the modelling of biomolecular complexes. Bioinformatics, 2006, 22, 2340-2347.
    • (2006) Bioinformatics , vol.22 , pp. 2340-2347
    • van Dijk, A.D.J.1    Bonvin, A.2
  • 20
    • 16344378407 scopus 로고    scopus 로고
    • Flexibilityof metal binding sites in proteins on a database scale
    • Babor, M.; Greenblatt, H. M.; Edelman, M.; Sobolev, V. Flexibilityof metal binding sites in proteins on a database scale. Proteins, 2005, 59, 221-230.
    • (2005) Proteins , vol.59 , pp. 221-230
    • Babor, M.1    Greenblatt, H.M.2    Edelman, M.3    Sobolev, V.4
  • 22
    • 84986522918 scopus 로고
    • ICM - A new method forprotein modeling and design - applications to docking and structureprediction from the distorted native conformation
    • Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM - A new method forprotein modeling and design - applications to docking and structureprediction from the distorted native conformation. J. Comput.Chem., 1994, 15, 488-506.
    • (1994) J. Comput.Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 23
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by globalenergy optimization in internal coordinates
    • Totrov, M.; Abagyan, R. Flexible protein-ligand docking by globalenergy optimization in internal coordinates. Proteins, 1997, 215-220.
    • (1997) Proteins , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 24
    • 0028854034 scopus 로고
    • Molecular recognition of receptor-sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor-sites using a genetic algorithm with a description of desolvation.J. Mol. Biol., 1995, 245, 43-53.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 25
    • 0031552362 scopus 로고    scopus 로고
    • Developmentand validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Developmentand validation of a genetic algorithm for flexible docking.J. Mol. Biol., 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 26
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckiangenetic algorithm and an empirical binding free energyfunction
    • Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W.E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckiangenetic algorithm and an empirical binding free energyfunction. 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
  • 27
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX incrementalconstruction algorithm for protein-ligand docking
    • Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FlexX incrementalconstruction algorithm for protein-ligand docking. Proteins, 1999, 37, 228-241.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 28
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: Efficientmolecular docking considering protein structure variations
    • Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: Efficientmolecular docking considering protein structure variations. J. Mol.Biol., 2001, 308, 377-395.
    • (2001) J. Mol.Biol. , vol.308 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 29
    • 1842532062 scopus 로고    scopus 로고
    • GEMDOCK: A generic evolutionarymethod for molecular docking
    • Yang, J. M.; Chen, C. C. GEMDOCK: A generic evolutionarymethod for molecular docking. Proteins, 2004, 55, 288-304.
    • (2004) Proteins , vol.55 , pp. 288-304
    • Yang, J.M.1    Chen, C.C.2
  • 30
    • 23144462493 scopus 로고    scopus 로고
    • MEDock: A web server forefficient prediction of ligand binding sites based on a novel optimizationalgorithm
    • Chang, D. T. H.; Oyang, Y. J.; Lin, J. H. MEDock: a web server forefficient prediction of ligand binding sites based on a novel optimizationalgorithm. Nucleic Acids Res., 2005, 33, W233-W238.
    • (2005) Nucleic Acids Res. , vol.33
    • Chang, D.T.H.1    Oyang, Y.J.2    Lin, J.H.3
  • 31
    • 33744826819 scopus 로고    scopus 로고
    • MolDock: A new technique forhigh-accuracy molecular docking
    • Thomsen, R.; Christensen, M. H. MolDock: A new technique forhigh-accuracy molecular docking. J. Med. Chem., 2006, 49, 3315-3321.
    • (2006) J. Med. Chem. , vol.49 , pp. 3315-3321
    • Thomsen, R.1    Christensen, M.H.2
  • 32
    • 33646102202 scopus 로고    scopus 로고
    • Tribe-PSO: A novel global optimizationAlgorithm and its application in molecular docking
    • Chen, K.; Li, T. H.; Cao, T. C. Tribe-PSO: A novel global optimizationAlgorithm and its application in molecular docking, Chemomet. Intell. Lab. Syst., 2006, 82, 248-259.
    • (2006) Intell. Lab. Syst. , vol.82 , pp. 248-259
    • Chen, K.1    Li, T.H.2    Cao, T.C.3
  • 33
    • 33846630833 scopus 로고    scopus 로고
    • SODOCK: Swarm optimization for highly flexible protein-liganddocking
    • Chen, H. M.; Liu, B. F.; Huang, H. L.; Hwang, S. F.; Ho, S. Y.SODOCK: Swarm optimization for highly flexible protein-liganddocking. J. Comput. Chem., 2007, 28, 612-623.
    • (2007) J. Comput. Chem. , vol.28 , pp. 612-623
    • Chen, H.M.1    Liu, B.F.2    Huang, H.L.3    Hwang, S.F.4    Ho, S.Y.5
  • 34
    • 6244283606 scopus 로고    scopus 로고
    • Critical evaluation of search algorithmsfor automated molecular docking and database screening
    • Ewing, T. J. A.; Kuntz, I. D. Critical evaluation of search algorithmsfor automated molecular docking and database screening. J.Comput. Chem., 1997, 18, 1175-1189.
    • (1997) J.Comput. Chem. , vol.18 , pp. 1175-1189
    • Ewing, T.J.A.1    Kuntz, I.D.2
  • 36
    • 76149120388 scopus 로고    scopus 로고
    • Software news and update autodock vina: Improving the speed and accuracy of docking with a new scoringfunction, efficient optimization, and multithreading
    • Trott, O.; Olson, A. J. Software news and update autodock vina: improving the speed and accuracy of docking with a new scoringfunction, efficient optimization, and multithreading. J. Comput.Chem., 31, 455-461.
    • J. Comput.Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 37
    • 0032015361 scopus 로고    scopus 로고
    • Identification of biologicalactivity profiles using substructural analysis and genetic algorithms
    • Gillet, V. J.; Willett, P.; Bradshaw, J. Identification of biologicalactivity profiles using substructural analysis and genetic algorithms.J. Chem. Inf. Comput. Sci., 1998, 38, 165-179.
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , pp. 165-179
    • Gillet, V.J.1    Willett, P.2    Bradshaw, J.3
  • 40
    • 0019525292 scopus 로고
    • Minimization by random search techniques
    • Solis, F. J.; Wets, R. J. B. Minimization by random search techniques.Math. Oper. Res., 1981, 6, 19-30.
    • (1981) Math. Oper. Res. , vol.6 , pp. 19-30
    • Solis, F.J.1    Wets, R.J.B.2
  • 41
    • 0027955787 scopus 로고
    • Biased probability monte-carlo conformationalsearches and electrostatic calculations for peptides and proteins
    • Abagyan, R.; Totrov, M. Biased probability monte-carlo conformationalsearches and electrostatic calculations for peptides and proteins.J. Mol. Biol., 1994, 235, 983-1002.
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 42
    • 0003853519 scopus 로고
    • Differential evolution - A simple and efficientadaptive scheme for global optimization over continuous spaces
    • International Computer Science Institute
    • Storn, R.; Price, K. Differential evolution - A simple and efficientadaptive scheme for global optimization over continuous spaces. Technical report; International Computer Science Institute 1995.
    • (1995) Technical report
    • Storn, R.1    Price, K.2
  • 44
    • 34247541511 scopus 로고    scopus 로고
    • Special issue on particle swarm optimization
    • Eberhart, R. C.; Shi, Y. H. Special issue on particle swarm optimization.IEEE Transact. Evol. Comput., 2004, 8, 201-203.
    • (2004) IEEE Transact. Evol. Comput. , vol.8 , pp. 201-203
    • Eberhart, R.C.1    Shi, Y.H.2
  • 45
    • 36348989005 scopus 로고    scopus 로고
    • PSO@AUTODOCK: A fast flexiblemolecular docking program based on swarm intelligence
    • Namasivayam, V.; Gunther, R. PSO@AUTODOCK: A fast flexiblemolecular docking program based on swarm intelligence.Chem. Biol. Drug Des., 2007, 70, 475-484.
    • (2007) Chem. Biol. Drug Des. , vol.70 , pp. 475-484
    • Namasivayam, V.1    Gunther, R.2
  • 46
    • 34548487766 scopus 로고    scopus 로고
    • Molecular docking withmulti-objective particle swarm optimization
    • Janson, S.; Merkle, D.; Middendorf, M. Molecular docking withmulti-objective particle swarm optimization. Appl. Soft Comput., 2008, 8, 666-675.
    • (2008) Appl. Soft Comput. , vol.8 , pp. 666-675
    • Janson, S.1    Merkle, D.2    Middendorf, M.3
  • 47
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparisonof current docking and scoring methods on systems of pharmaceuticalrelevance
    • Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparisonof current docking and scoring methods on systems of pharmaceuticalrelevance. Proteins-Struct. Funct. Bioinfor., 2004, 56, 235-249.
    • (2004) Proteins-Struct. Funct. Bioinfor. , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 48
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of docking performance: Comparative data on docking algorithms. J.Med. Chem., 2004, 47, 558-565.
    • (2004) J.Med. Chem. , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 49
    • 1942471391 scopus 로고    scopus 로고
    • Assessingscoring functions for protein-ligand interactions
    • Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L. Assessingscoring 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
  • 50
    • 66149103553 scopus 로고    scopus 로고
    • Comparativeassessment of scoring functions on a diverse test set
    • Cheng, T. J.; Li, X.; Li, Y.; Liu, Z. H.; Wang, R. X. Comparativeassessment of scoring functions on a diverse test set. J. Chem. Inf.Model., 2009, 49, 1079-1093.
    • (2009) J. Chem. Inf.Model. , vol.49 , pp. 1079-1093
    • Cheng, T.J.1    Li, X.2    Li, Y.3    Liu, Z.H.4    Wang, R.X.5
  • 51
    • 10044294023 scopus 로고    scopus 로고
    • An extensive testof 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • Wang, R. X.; Lu, Y. P.; Fang, X. L.; Wang, S. M. An extensive testof 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci., 2004, 44, 2114-2125.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 2114-2125
    • Wang, R.X.1    Lu, Y.P.2    Fang, X.L.3    Wang, S.M.4
  • 52
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11scoring functions for molecular docking
    • Wang, R. X.; Lu, Y. P.; Wang, S. M. Comparative evaluation of 11scoring functions for molecular docking. J. Med. Chem., 2003, 46, 2287-2303.
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.X.1    Lu, Y.P.2    Wang, S.M.3
  • 53
    • 0035438402 scopus 로고    scopus 로고
    • How does consensus scoring work forvirtual library screening? An idealized computer experiment
    • Wang, R. X.; Wang, S. M. How does consensus scoring work forvirtual library screening? An idealized computer experiment. J.Chem. Inf. Comput. Sci., 2001, 41, 1422-1426.
    • (2001) J.Chem. Inf. Comput. Sci. , vol.41 , pp. 1422-1426
    • Wang, R.X.1    Wang, S.M.2
  • 54
    • 69549118627 scopus 로고    scopus 로고
    • Testing assumptionsand hypotheses for rescoring success in protein-ligand docking
    • O'Boyle, N. M.; Liebeschuetz, J. W.; Cole, J. C. Testing assumptionsand hypotheses for rescoring success in protein-ligand docking.J. Chem. Inf. Model., 2009, 49, 1871-1878.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1871-1878
    • O'Boyle, N.M.1    Liebeschuetz, J.W.2    Cole, J.C.3
  • 56
    • 34447521097 scopus 로고
    • Correlation of biologicalactivity of phenoxyacetic acids with hammett substituent constantsand partition coefficients
    • Hansch, C.; Maloney, P. P.; Fujita, T. Correlation of biologicalactivity of phenoxyacetic acids with hammett substituent constantsand partition coefficients. Nature, 1962, 194, 178-&.
    • (1962) Nature , vol.194 , pp. 178
    • Hansch, C.1    Maloney, P.P.2    Fujita, T.3
  • 57
    • 33947716119 scopus 로고    scopus 로고
    • A semiempiricalfree energy force field with charge-based desolvation
    • Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A semiempiricalfree energy force field with charge-based desolvation. J.Comput. Chem., 2007, 28, 1145-1152.
    • (2007) J.Comput. Chem. , vol.28 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 58
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based bindingaffinity prediction
    • Wang, R. X.; Lai, L. H.; Wang, S. M. Further development and validation of empirical scoring functions for structure-based bindingaffinity prediction. J. Comput.-Aided Mol. Des., 2002, 16, 11-26.
    • (2002) J. Comput.-Aided Mol. Des. , vol.16 , pp. 11-26
    • Wang, R.X.1    Lai, L.H.2    Wang, S.M.3
  • 59
    • 0028155689 scopus 로고
    • New method for predictingbinding-affinity in computer-aided drug design
    • Åqvist, J.; Medina, C.; Samuelsson, J. E. New method for predictingbinding-affinity in computer-aided drug design. Protein Eng., 1994, 7, 385-391.
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 60
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity predictionby linear interaction energy methods
    • Hansson, T.; Marelius, J.; Åqvist, J. Ligand binding affinity predictionby linear interaction energy methods. J. Comput.-Aided Mol.Des., 1998, 12, 27-35.
    • (1998) J. Comput.-Aided Mol.Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Åqvist, J.3
  • 62
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligandbinding
    • Massova, I.; Kollman, P. A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligandbinding. Pers. Drug Discov. Des., 2000, 18, 113-135.
    • (2000) Pers. Drug Discov. Des. , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 63
    • 0001672288 scopus 로고
    • Chemical and electrochemical electron-transfertheory
    • Marcus, R. A. Chemical and electrochemical electron-transfertheory. Annu. Rev. Phys. Chem., 1964, 15, 155-196.
    • (1964) Annu. Rev. Phys. Chem. , vol.15 , pp. 155-196
    • Marcus, R.A.1
  • 64
    • 0027390460 scopus 로고
    • The contribution of cross-links to proteinstability - a normal mode analysis of the configurational entropy of the native-state
    • Tidor, B.; Karplus, M. The contribution of cross-links to proteinstability - a normal mode analysis of the configurational entropy of the native-state. Proteins, 1993, 15, 71-79.
    • (1993) Proteins , vol.15 , pp. 71-79
    • Tidor, B.1    Karplus, M.2
  • 65
    • 0000127140 scopus 로고
    • Method for estimating the configurationalentropy of macromolecules
    • Karplus, M.; Kushick, J. N. Method for estimating the configurationalentropy of macromolecules. Macromolecules, 1981, 14, 325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 66
    • 33745405015 scopus 로고    scopus 로고
    • High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing
    • Brown, S. P.; Muchmore, S. W. High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing. J. Chem. Inf.Model., 2006, 46, 999-1005.
    • (2006) J. Chem. Inf.Model. , vol.46 , pp. 999-1005
    • Brown, S.P.1    Muchmore, S.W.2
  • 67
    • 34547666868 scopus 로고    scopus 로고
    • Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA
    • Brown, S. P.; Muchmore, S. W. Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA. J. Chem. Inf. Model., 2007, 47, 1493-1503.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1493-1503
    • Brown, S.P.1    Muchmore, S.W.2
  • 68
    • 66249097011 scopus 로고    scopus 로고
    • Large-scale application of highthroughputmolecular mechanics with Poisson-Boltzmann surfacearea for routine physics-based scoring of protein-ligand complexes
    • Brown, S. P.; Muchmore, S. W. Large-scale application of highthroughputmolecular mechanics with Poisson-Boltzmann surfacearea for routine physics-based scoring of protein-ligand complexes.J. Med. Chem., 2009, 52, 3159-3165.
    • (2009) J. Med. Chem. , vol.52 , pp. 3159-3165
    • Brown, S.P.1    Muchmore, S.W.2
  • 69
    • 50249114683 scopus 로고    scopus 로고
    • An improved relaxedcomplex scheme for receptor flexibility in computer-aided drug design
    • Amaro, R. E.; Baron, R.; McCammon, J. A. An improved relaxedcomplex scheme for receptor flexibility in computer-aided drug design.J. Comput.-Aided Mol. Des., 2008, 22, 693-705.
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 693-705
    • Amaro, R.E.1    Baron, R.2    McCammon, J.A.3
  • 70
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: The relaxed complex scheme
    • Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A.Computational drug design accommodating receptor flexibility: The relaxed complex scheme. J. Am. Chem. Soc., 2002, 124, 5632-5633.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5632-5633
    • Lin, J.H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 71
    • 0037231646 scopus 로고    scopus 로고
    • Therelaxed complex method: Accommodating receptor flexibility fordrug design with an improved scoring scheme
    • Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. Therelaxed complex method: Accommodating receptor flexibility fordrug design with an improved scoring scheme. Biopolymers, 2003, 68, 47-62.
    • (2003) Biopolymers , vol.68 , pp. 47-62
    • Lin, J.H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 72
    • 0029836953 scopus 로고    scopus 로고
    • Discoveringhigh-affinity ligands for proteins: SAR by NMR
    • Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Discoveringhigh-affinity ligands for proteins: SAR by NMR. Science, 1996, 274, 1531-1534.
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 73
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • Adcock, S. A.; McCammon, J. A. Molecular dynamics: Survey of methods for simulating the activity of proteins. Chem. Rev., 2006, 106, 1589-1615.
    • (2006) Chem. Rev. , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 76
    • 33745202841 scopus 로고    scopus 로고
    • Optimization and computational evaluation of a series of potential active site inhibitorsof the V82F/I84V drug-resistant mutant of HIV-1 protease: Anapplication of the relaxed complex method of structure-based drugdesign
    • Perryman, A. L.; Lin, J. H.; McCammon, J. A. Optimization and computational evaluation of a series of potential active site inhibitorsof the V82F/I84V drug-resistant mutant of HIV-1 protease: Anapplication of the relaxed complex method of structure-based drugdesign. Chem. Biol. Drug Des., 2006, 67, 336-345.
    • (2006) Chem. Biol. Drug Des. , vol.67 , pp. 336-345
    • Perryman, A.L.1    Lin, J.H.2    McCammon, J.A.3
  • 77
    • 33750139049 scopus 로고    scopus 로고
    • In-situ synthesis of atacrine-triazole-based inhibitor of acetylcholinesterase: Configurational selection imposed by steric interactions
    • Senapati, S.; Cheng, Y. H.; McCammon, J. A. In-situ synthesis of atacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions. J. Med. Chem., 2006, 49, 6222-6230.
    • (2006) J. Med. Chem. , vol.49 , pp. 6222-6230
    • Senapati, S.1    Cheng, Y.H.2    McCammon, J.A.3
  • 78
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potentialnovel 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 potentialnovel 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
  • 79
    • 4544310320 scopus 로고    scopus 로고
    • Modeling correlated main-chain motions in proteins for flexiblemolecular recognition
    • Zavodszky, M. I.; Ming, L.; Thorpe, M. F.; Day, A. R.; Kuhn, L.A. Modeling correlated main-chain motions in proteins for flexiblemolecular recognition. Proteins, 2004, 57, 243-261.
    • (2004) Proteins , vol.57 , pp. 243-261
    • Zavodszky, M.I.1    Ming, L.2    Thorpe, M.F.3    Day, A.R.4    Kuhn, L.A.5
  • 80
    • 45749139232 scopus 로고    scopus 로고
    • Protein-ligand docking accounting forreceptor side chain and global flexibility in normal modes: Evaluationon kinase inhibitor cross docking
    • May, A.; Zacharias, M. Protein-ligand docking accounting forreceptor side chain and global flexibility in normal modes: Evaluationon kinase inhibitor cross docking. J. Med. Chem., 2008, 51, 3499-3506.
    • (2008) J. Med. Chem. , vol.51 , pp. 3499-3506
    • May, A.1    Zacharias, M.2
  • 81
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequencynormal modes to efficiently allow for global flexibility during systematicprotein-protein docking
    • May, A.; Zacharias, M. Energy minimization in low-frequencynormal modes to efficiently allow for global flexibility during systematicprotein-protein docking. Proteins, 2008, 70, 794-809.
    • (2008) Proteins , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 82
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand dockingand virtual screening to protein kinases
    • Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand dockingand virtual screening to protein kinases. J. Mol. Biol., 2004, 337, 209-225.
    • (2004) J. Mol. Biol. , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 83
    • 65249120827 scopus 로고    scopus 로고
    • Consistent improvement of cross-docking results using binding site ensembles generated withelastic network normal modes
    • Rueda, M.; Bottegoni, G.; Abagyan, R. Consistent improvement of cross-docking results using binding site ensembles generated withelastic network normal modes. J. Chem. Inf. Model., 2009, 49, 716-725.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 716-725
    • Rueda, M.1    Bottegoni, G.2    Abagyan, R.3
  • 86
    • 67849122312 scopus 로고    scopus 로고
    • SLITHER: A web server for generating contiguous conformations of substratemolecules entering into deep active sites of proteins or migratingthrough channels in membrane transporters
    • Lee, P. H.; Kuo, K. L.; Chu, P. Y.; Liu, E. M.; Lin, J. H. SLITHER: a web server for generating contiguous conformations of substratemolecules entering into deep active sites of proteins or migratingthrough channels in membrane transporters. Nucleic Acids Res., 2009, 37, W559-W564.
    • (2009) Nucleic Acids Res. , vol.37
    • Lee, P.H.1    Kuo, K.L.2    Chu, P.Y.3    Liu, E.M.4    Lin, J.H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.