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Volumn , Issue , 2011, Pages 99-117

Receptor flexibility in ligand docking and virtual screening

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EID: 84876886763     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.2174/978160805142711101010099     Document Type: Chapter
Times cited : (6)

References (158)
  • 1
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S.J. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discov. 2003, 2, 527-541.
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 2
    • 27644453181 scopus 로고    scopus 로고
    • The challenge of considering receptor flexibility in ligand docking and virtual screening
    • Cavasotto, C.N.; Orry, A.J.; Abagyan, R. The challenge of considering receptor flexibility in ligand docking and virtual screening. Curr. Comput-Aided Drug Design 2005, 1, 423-440.
    • (2005) Curr. Comput-Aided Drug Design , vol.1 , pp. 423-440
    • Cavasotto, C.N.1    Orry, A.J.2    Abagyan, R.3
  • 3
    • 0037154793 scopus 로고    scopus 로고
    • ENZYMOLOGY: A moving story
    • Falke, J.J. ENZYMOLOGY: A moving story. Science 2002, 295, 1480-1481.
    • (2002) Science , vol.295 , pp. 1480-1481
    • Falke, J.J.1
  • 4
    • 28844493408 scopus 로고    scopus 로고
    • Musings on ADME predictions and structure-activity relations
    • Testa, B.; Vistoli, G.; Pedretti, A. Musings on ADME predictions and structure-activity relations. Chem. Biodivers 2005, 2, 1411-1427.
    • (2005) Chem. Biodivers , vol.2 , pp. 1411-1427
    • Testa, B.1    Vistoli, G.2    Pedretti, A.3
  • 5
    • 1442351132 scopus 로고    scopus 로고
    • J. Mol. Biol.
    • Cavasotto, C.N.; Abagyan, R.A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 2004, 337, 209-225.
    • (2004) , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 6
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson, J.A.; Jalaie, M.; Robertson, D.H.; Lewis, R.A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
    • (2004) J. Med. Chem. , vol.47 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 7
    • 27144484954 scopus 로고    scopus 로고
    • Receptor flexibility in de novo ligand design and docking
    • Alberts, I.L.; Todorov, N.P.; Dean, P.M. Receptor flexibility in de novo ligand design and docking. J. Med. Chem. 2005, 48, 6585-6596.
    • (2005) J. Med. Chem. , vol.48 , pp. 6585-6596
    • Alberts, I.L.1    Todorov, N.P.2    Dean, P.M.3
  • 9
    • 35348821202 scopus 로고    scopus 로고
    • Virtual screening strategies in drug discovery
    • McInnes, C. Virtual screening strategies in drug discovery. Curr. Opin. Chem. Biol. 2007, 11, 494-502.
    • (2007) Curr. Opin. Chem. Biol. , vol.11 , pp. 494-502
    • McInnes, C.1
  • 10
    • 54749115273 scopus 로고    scopus 로고
    • Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility
    • Cavasotto, C.N.; Singh, N. Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility. Current Computer-Aided Drug Design 2008, 4, 221-234.
    • (2008) Current Computer-Aided Drug Design , vol.4 , pp. 221-234
    • Cavasotto, C.N.1    Singh, N.2
  • 11
    • 63149162777 scopus 로고    scopus 로고
    • Managing protein flexibility in docking and its applications
    • B-Rao, C.; Subramanian, J.; Sharma, S.D. Managing protein flexibility in docking and its applications. Drug Discov. Today 2009, 14, 394-400.
    • (2009) Drug Discov. Today , vol.14 , pp. 394-400
    • B-rao, C.1    Subramanian, J.2    Sharma, S.D.3
  • 12
    • 0034813214 scopus 로고    scopus 로고
    • Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase
    • Fritz, T.A.; Tondi, D.; Finer-Moore, J.S.; Costi, M.P.; Stroud, R.M. Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase. Chem. Biol. 2001, 8, 981-995.
    • (2001) Chem. Biol. , vol.8 , pp. 981-995
    • Fritz, T.A.1    Tondi, D.2    Finer-moore, J.S.3    Costi, M.P.4    Stroud, R.M.5
  • 13
    • 0034642532 scopus 로고    scopus 로고
    • Cyclin-dependent kinase inhibitors: useful targets in cell cycle regulation
    • Sielecki, T.M.; Boylan, J.F.; Benfield, P.A.; Trainor, G.L. Cyclin-dependent kinase inhibitors: useful targets in cell cycle regulation. J. Med. Chem. 2000, 43, 1-18.
    • (2000) J. Med. Chem. , vol.43 , pp. 1-18
    • Sielecki, T.M.1    Boylan, J.F.2    Benfield, P.A.3    Trainor, G.L.4
  • 16
    • 33745880692 scopus 로고    scopus 로고
    • Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase
    • Frembgen-Kesner, T.; Elcock, A.H. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. J. Mol. Biol. 2006, 359, 202-214.
    • (2006) J. Mol. Biol. , vol.359 , pp. 202-214
    • Frembgen-kesner, T.1    Elcock, A.H.2
  • 17
    • 33947662384 scopus 로고    scopus 로고
    • Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system
    • Bowman, A.L.; Lerner, M.G.; Carlson, H.A. Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system. J. Am. Chem. Soc. 2007, 129, 3634-3640.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 3634-3640
    • Bowman, A.L.1    Lerner, M.G.2    Carlson, H.A.3
  • 18
    • 0024498518 scopus 로고
    • Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding
    • Birdsall, B.; Feeney, J.; Tendler, S.J.; Hammond, S.J.; Roberts, G.C. Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding. 1989, 7, 2297-2305.
    • (1989) , vol.7 , pp. 2297-2305
    • Birdsall, B.1    Feeney, J.2    Tendler, S.J.3    Hammond, S.J.4    Roberts, G.C.5
  • 20
    • 33846635484 scopus 로고    scopus 로고
    • Targeting structural flexibility in HIV-1 protease inhibitor binding
    • Hornak, V.; Simmerling, C. Targeting structural flexibility in HIV-1 protease inhibitor binding. Drug Discov. Today 2007, 12, 132-138.
    • (2007) Drug Discov. Today , vol.12 , pp. 132-138
    • Hornak, V.1    Simmerling, C.2
  • 21
    • 52049093435 scopus 로고    scopus 로고
    • A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket
    • Damm, K.L.; Ung, P.M.; Quintero, J.J.; Gestwicki, J.E.; Carlson, H.A. A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket. Biopolymers 2008, 89, 643-652.
    • (2008) Biopolymers , vol.89 , pp. 643-652
    • Damm, K.L.1    Ung, P.M.2    Quintero, J.J.3    Gestwicki, J.E.4    Carlson, H.A.5
  • 23
    • 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
  • 25
    • 84892166712 scopus 로고
    • Einfluss der configuration auf die wirkung derenzyme
    • Fischer, E. Einfluss der configuration auf die wirkung derenzyme. Ber. Dtsch. Chem. Ges. 1894, 27, 2985-2993.
    • (1894) Ber. Dtsch. Chem. Ges. , vol.27 , pp. 2985-2993
    • Fischer, E.1
  • 26
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland, D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 1958, 44, 98-104.
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 27
    • 0000013948 scopus 로고
    • Protein structure and enzyme activity
    • Academic Press: New York
    • Linderstrøm-Lang, K.U.; Schellman, J.A. Protein structure and enzyme activity. Academic Press: New York: 1959; Vol. 1, pp. 443-510.
    • (1959) , vol.1 , pp. 443-510
    • Linderstrøm-lang, K.U.1    Schellman, J.A.2
  • 28
    • 0008306770 scopus 로고
    • Formation of the secondary and tertiary structure of enzymes
    • Straub, F.B. Formation of the secondary and tertiary structure of enzymes. Adv. Enzymol. Relat. Areas Mol. Biol. 1964, 26, 89-114.
    • (1964) Adv. Enzymol. Relat. Areas Mol. Biol. , vol.26 , pp. 89-114
    • Straub, F.B.1
  • 29
    • 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
  • 31
    • 49549092691 scopus 로고    scopus 로고
    • Protein-protein interactions: from global to local analyses
    • Kelly, W.; Stumpf, M. Protein-protein interactions: from global to local analyses. Curr. Opin. Biotechnol. 2008, 19, 396-403.
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 396-403
    • Kelly, W.1    Stumpf, M.2
  • 32
    • 85056052381 scopus 로고    scopus 로고
    • Screening outside the catalytic site: Inhibition of macromolecular interactions through structure-based virtual ligand screening experiments
    • Sperandio, O.; Miteva, M.A.; Segers, K.; Nicolaes, G.; Villoutreix, B.O. Screening outside the catalytic site: Inhibition of macromolecular interactions through structure-based virtual ligand screening experiments. The Open Biochemistry Journal 2008, 2, 29-37.
    • (2008) The Open Biochemistry Journal , vol.2 , pp. 29-37
    • Sperandio, O.1    Miteva, M.A.2    Segers, K.3    Nicolaes, G.4    Villoutreix, B.O.5
  • 33
    • 34548394483 scopus 로고    scopus 로고
    • Human protein-protein interaction networks and the value for drug discovery
    • Ruffner, H.; Bauer, A.; Bouwmeester, T. Human protein-protein interaction networks and the value for drug discovery. Drug Discov. Today 2007, 12, 709-716
    • (2007) Drug Discov. Today , vol.12 , pp. 709-716
    • Ruffner, H.1    Bauer, A.2    Bouwmeester, T.3
  • 35
    • 0026323860 scopus 로고
    • The crystal structures of recombinant glycosylated human renin alone and in complex with a transition state analogue inhibitor
    • Rahuel, J.; Priestle, J.P.; Grutter, M.G. The crystal structures of recombinant glycosylated human renin alone and in complex with a transition state analogue inhibitor. J. Struct. Biol. 1991, 107, 227-236
    • (1991) J. Struct. Biol. , vol.107 , pp. 227-236
    • Rahuel, J.1    Priestle, J.P.2    Grutter, M.G.3
  • 36
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: a matter of preexisting populations
    • Ma, B.; Shatsky, M.; Wolfson, H.J.; Nussinov, R. Multiple diverse ligands binding at a single protein site: a matter of preexisting populations. Protein Sci. 2002, 11, 184-197
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 38
    • 0028924567 scopus 로고
    • Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors
    • Esnouf, R.; Ren, J.; Ross, C.; Jones, Y.; Stammers, D.; Stuart, D. Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors. Nat. Struct. Biol. 1995, 2, 303-308.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 303-308
    • Esnouf, R.1    Ren, J.2    Ross, C.3    Jones, Y.4    Stammers, D.5    Stuart, D.6
  • 39
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
    • Murray, C.W.; Baxter, C.A.; Frenkel, A.D. The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase. J. Comput. Aided Mol. Des. 1999, 13, 547-562.
    • (1999) J. Comput. Aided Mol. Des. , vol.13 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 40
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • McGovern, S.L.; Shoichet, B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 2003, 46, 2895-2907.
    • (2003) J. Med. Chem. , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 41
    • 2442706574 scopus 로고    scopus 로고
    • Receptor flexibility in the in silico screening of reagents in the S1' pocket of human collagenase
    • Kallblad, P.; Todorov, N.P.; Willems, H.M.; Alberts, I.L. Receptor flexibility in the in silico screening of reagents in the S1' pocket of human collagenase. J. Med. Chem. 2004, 47, 2761-2767.
    • (2004) J. Med. Chem. , vol.47 , pp. 2761-2767
    • Kallblad, P.1    Todorov, N.P.2    Willems, H.M.3    Alberts, I.L.4
  • 42
    • 33748759844 scopus 로고    scopus 로고
    • Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors
    • Floquet, N.; Marechal, J.D.; Badet-Denisot, M.A.; Robert, C.H.; Dauchez, M.; Perahia, D. Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors. FEBS Lett. 2006, 580, 5130-5136.
    • (2006) FEBS Lett. , vol.580 , pp. 5130-5136
    • Floquet, N.1    Marechal, J.D.2    Badet-denisot, M.A.3    Robert, C.H.4    Dauchez, M.5    Perahia, D.6
  • 43
    • 58149103168 scopus 로고    scopus 로고
    • Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site
    • Floquet, N.; Durand, P.; Maigret, B.; Badet, B.; Badet-Denisot, M.A.; Perahia, D. Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site. J. Mol. Biol. 2009, 385, 653-664.
    • (2009) J. Mol. Biol. , vol.385 , pp. 653-664
    • Floquet, N.1    Durand, P.2    Maigret, B.3    Badet, B.4    Badet-denisot, M.A.5    Perahia, D.6
  • 44
    • 65249120827 scopus 로고    scopus 로고
    • Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes
    • Rueda, M.; Bottegoni, G.; Abagyan, R. Consistent improvement of cross-docking results using binding site ensembles generated with elastic 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
  • 45
    • 77955627131 scopus 로고    scopus 로고
    • How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
    • DOI 10.1007/s00249-010-0592-0
    • Sperandio, O.; Mouawad, L.; Pinto, E.; Villoutreix, B.O.; Perahia, D.; Miteva, M.A. How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. 2010, DOI 10.1007/s00249-010-0592-0.
    • (2010)
    • Sperandio, O.1    Mouawad, L.2    Pinto, E.3    Villoutreix, B.O.4    Perahia, D.5    Miteva, M.A.6
  • 47
    • 21244479779 scopus 로고    scopus 로고
    • Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
    • Barril, X.; Morley, S.D. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J. Med. Chem. 2005, 48, 4432-4443.
    • (2005) J. Med. Chem. , vol.48 , pp. 4432-4443
    • Barril, X.1    Morley, S.D.2
  • 48
    • 33746924045 scopus 로고    scopus 로고
    • Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and betasecretase
    • Polgar, T.; Keseru, G.M. Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and betasecretase. J. Chem. Inf. Model. 2006, 46, 1795-1805.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1795-1805
    • Polgar, T.1    Keseru, G.M.2
  • 49
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: a practical alternative
    • Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 2008, 18, 178-184.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 52
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 54
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel, R.M.; Kuntz, I.D.; Oshiro, C.M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-440.
    • (1997) J. Mol. Biol. , vol.266 , pp. 424-440
    • Knegtel, R.M.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 55
    • 4744365803 scopus 로고    scopus 로고
    • Soft docking and multiple receptor conformations in virtual screening
    • Ferrari, A.M.; Wei, B.Q.; Costantino, L.; Shoichet, B.K. Soft docking and multiple receptor conformations in virtual screening. J. Med. Chem. 2004, 47, 5076-5084.
    • (2004) J. Med. Chem. , vol.47 , pp. 5076-5084
    • Ferrari, A.M.1    Wei, B.Q.2    Costantino, L.3    Shoichet, B.K.4
  • 56
    • 33244470695 scopus 로고    scopus 로고
    • rand canonical Monte Carlo simulation of ligand-protein binding
    • Clark, M.; Guarnieri, F.; Shkurko, I.; Wiseman, J. Grand canonical Monte Carlo simulation of ligand-protein binding. J. Chem. Inf. Model. 2006, 46, 231-242.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 231-242
    • Clark, M.1    Guarnieri, F.2    Shkurko, I.3    Wiseman, J.4
  • 58
    • 0024789103 scopus 로고
    • A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method
    • Kawai, H.; Kikuchi, T.; Okamoto, Y. A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method. Protein Eng. 1989, 3, 85-94.
    • (1989) Protein Eng. , vol.3 , pp. 85-94
    • Kawai, H.1    Kikuchi, T.2    Okamoto, Y.3
  • 59
    • 0025635729 scopus 로고
    • Distance-constrained molecular docking by simulated annealing
    • Yue, S.Y. Distance-constrained molecular docking by simulated annealing. Protein Eng. 1990, 4, 177-184.
    • (1990) Protein Eng. , vol.4 , pp. 177-184
    • Yue, S.Y.1
  • 60
    • 0001246354 scopus 로고    scopus 로고
    • Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP-substrate complex
    • Caflisch, A.; Fischer, S.; Karplus, M. Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP-substrate complex. 1997, 18, 723-743.
    • (1997) , vol.18 , pp. 723-743
    • Caflisch, A.1    Fischer, S.2    Karplus, M.3
  • 61
    • 0042282803 scopus 로고    scopus 로고
    • FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
    • Taylor, R.D.; Jewsbury, P.J.; Essex, J.W. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J. Comput. Chem. 2003, 24, 1637-1656.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1637-1656
    • Taylor, R.D.1    Jewsbury, P.J.2    Essex, J.W.3
  • 62
    • 58149094776 scopus 로고    scopus 로고
    • RosettaLigand docking with full ligand and receptor flexibility
    • Davis, I.W.; Baker, D. RosettaLigand docking with full ligand and receptor flexibility. J. Mol. Biol. 2009, 385, 381-392.
    • (2009) J. Mol. Biol. , vol.385 , pp. 381-392
    • Davis, I.W.1    Baker, D.2
  • 64
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G.; 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. 1999, 19, 1639-1662.
    • (1999) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 65
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R. Development and 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
  • 67
    • 34247197110 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0
    • Corbeil, C.R.; Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J. Chem. Inf. Model. 2007, 47, 435-449.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 435-449
    • Corbeil, C.R.1    Englebienne, P.2    Moitessier, N.3
  • 68
    • 27744464203 scopus 로고    scopus 로고
    • Normal mode analysis: theory and applications to biological and chemical systems
    • Chapman & Hall, London
    • Cui, Q.; Bahar, I., Normal mode analysis: theory and applications to biological and chemical systems. Chapman & Hall, London: 2006.
    • (2006)
    • Cui, Q.1    Bahar, I.2
  • 69
    • 0029374782 scopus 로고
    • Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin
    • Perahia, D.; Mouawad, L. Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Comput. Chem. 1995, 19, 241-246.
    • (1995) Comput. Chem. , vol.19 , pp. 241-246
    • Perahia, D.1    Mouawad, L.2
  • 70
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto, C.N.; Kovacs, J.A.; Abagyan, R.A. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 2005, 127, 9632-9640.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 71
    • 9244235496 scopus 로고    scopus 로고
    • A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor
    • Tatsumi, R.; Fukunishi, Y.; Nakamura, H. A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. J. Comput. Chem. 2004, 25, 1995-2005.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1995-2005
    • Tatsumi, R.1    Fukunishi, Y.2    Nakamura, H.3
  • 72
    • 73649109875 scopus 로고    scopus 로고
    • Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR)
    • Floquet, N.; M'Kadmi, C.; Perahia, D.; Gagne, D.; Berge, G.; Marie, J.; Baneres, J.L.; Galleyrand, J.C.; Fehrentz, J.A.; Martinez, J. Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR). J. Mol. Biol. 2010 395, 769-778.
    • (2010) J. Mol. Biol. , vol.395 , pp. 769-778
    • Floquet N.1    M'Kadmi, C.2    Perahia, D.3    Gagne, D.4    Berge, G.5    Marie, J.6    Baneres, J.L.7    Galleyrand, J.C.8    Fehrentz, J.A.9    Martinez, J.10
  • 73
    • 42749088112 scopus 로고    scopus 로고
    • Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis
    • Sander, T.; Liljefors, T.; Balle, T. Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. J. Mol. Graph. Model. 2008, 26, 1259-1268.
    • (2008) J. Mol. Graph. Model. , vol.26 , pp. 1259-1268
    • Sander, T.1    Liljefors, T.2    Balle, T.3
  • 74
    • 45749139232 scopus 로고    scopus 로고
    • Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking
    • May, A.; Zacharias, M. Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on 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
  • 76
    • 1542316339 scopus 로고    scopus 로고
    • Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP
    • Zacharias, M. Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. Proteins 2004, 54, 759-767.
    • (2004) Proteins , vol.54 , pp. 759-767
    • Zacharias, M.1
  • 77
    • 64749106204 scopus 로고    scopus 로고
    • Molecular modeling, dynamics and docking studies of purine nucleoside phosphorylase from Streptococcus pyogenes
    • Timmers, L.F.; Caceres, R.A.; Dias, R.; Basso, L.A.; Santos, D.S.; de Azevedo, W.F., Jr. Molecular modeling, dynamics and docking studies of purine nucleoside phosphorylase from Streptococcus pyogenes. Biophys. Chem. 2009, 142, 7-16.
    • (2009) Biophys. Chem. , vol.142 , pp. 7-16
    • Timmers, L.F.1    Caceres, R.A.2    Dias, R.3    Basso, L.A.4    Santos, D.S.5    De Azevedo Jr, W.F.6
  • 78
    • 34250827919 scopus 로고    scopus 로고
    • Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries
    • Chang, M.W.; Lindstrom, W.; Olson, A.J.; Belew, R.K. Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries. J. Chem. Inf. Model. 2007, 47, 1258-1262.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1258-1262
    • Chang, M.W.1    Lindstrom, W.2    Olson, A.J.3    Belew, R.K.4
  • 79
    • 0027219536 scopus 로고
    • Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase
    • Caflisch, A.; Miranker, A.; Karplus, M. Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. J. Med. Chem. 1993, 36, 2142-2167.
    • (1993) J. Med. Chem. , vol.36 , pp. 2142-2167
    • Caflisch, A.1    Miranker, A.2    Karplus, M.3
  • 80
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
    • Elber, R.; Karplusm, M. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 1990, 112, 9161-9175.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 9161-9175
    • Elber, R.1    Karplusm, M.2
  • 81
    • 0041781898 scopus 로고    scopus 로고
    • Detailed analysis of grid-based molecular docking: A case study of CDOCKER-a CHARMM-based MD docking algorithm
    • Wu, G.; Robertson, D.H.; Brooks, C.L.I.; Vieth, M. Detailed analysis of grid-based molecular docking: A case study of CDOCKER-a CHARMM-based MD docking algorithm. J. Comput. Chem. 2003, 24, 1549-1562.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1549-1562
    • Wu, G.1    Robertson, D.H.2    Brooks, C.L.I.3    Vieth, M.4
  • 82
    • 0034632804 scopus 로고    scopus 로고
    • DoMCoSAR: a novel approach for establishing the docking mode that is consistent with the structure-activity relationship. Application to HIV-1 protease inhibitors and VEGF receptor tyrosine kinase inhibitors
    • Vieth, M.; Cummins, D.J. DoMCoSAR: a novel approach for establishing the docking mode that is consistent with the structure-activity relationship. Application to HIV-1 protease inhibitors and VEGF receptor tyrosine kinase inhibitors. J. Med. Chem. 2000, 43, 3020-3032.
    • (2000) J. Med. Chem. , vol.43 , pp. 3020-3032
    • Vieth, M.1    Cummins, D.J.2
  • 83
    • 2542543615 scopus 로고    scopus 로고
    • SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy
    • Wu, G.; Vieth, M. SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy. J. Med. Chem. 2004, 47, 3142-3148.
    • (2004) J. Med. Chem. , vol.47 , pp. 3142-3148
    • Wu, G.1    Vieth, M.2
  • 84
    • 23944459025 scopus 로고    scopus 로고
    • A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
    • Khandelwal, A.; Lukacova, V.; Comez, D.; Kroll, D. M.; Raha, S.; Balaz, S. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J. Med. Chem. 2005, 48, 5437-5447.
    • (2005) J. Med. Chem. , vol.48 , pp. 5437-5447
    • Khandelwal, A.1    Lukacova, V.2    Comez, D.3    Kroll, D.M.4    Raha, S.5    Balaz, S.6
  • 85
    • 33244496700 scopus 로고    scopus 로고
    • New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2
    • Ferrara, P.; Curioni, A.; Vangrevelinghe, E.; Meyer, T.; Mordasini, T.; Andreoni, W.; Acklin, P.; Jacoby, E. New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2. J. Chem. Inf. Model. 2006, 46, 254-263.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 254-263
    • Ferrara, P.1    Curioni, A.2    Vangrevelinghe, E.3    Meyer, T.4    Mordasini, T.5    Andreoni, W.6    Acklin, P.7    Jacoby, E.8
  • 87
    • 0033168443 scopus 로고    scopus 로고
    • Flexible ligand docking: a multistep strategy approach
    • Wang, J.; Kollman, P.A.; Kuntz, I.D. Flexible ligand docking: a multistep strategy approach. Proteins 1999, 36, 1-19.
    • (1999) Proteins , vol.36 , pp. 1-19
    • Wang, J.1    Kollman, P.A.2    Kuntz, I.D.3
  • 88
    • 33745088619 scopus 로고    scopus 로고
    • Use of an induced fit receptor structure in virtual screening
    • Sherman, W.; Beard, H.S.; Farid, R. Use of an induced fit receptor structure in virtual screening. Chem. Biol. Drug. Des. 2006, 67, 83-84.
    • (2006) Chem. Biol. Drug. Des. , vol.67 , pp. 83-84
    • Sherman, W.1    Beard, H.S.2    Farid, R.3
  • 89
    • 37349085453 scopus 로고    scopus 로고
    • A flexible approach to induced fit docking
    • Nabuurs, S.B.; Wagener, M.; de Vlieg, J. A flexible approach to induced fit docking. J. Med. Chem. 2007, 50, 6507-6518.
    • (2007) J. Med. Chem. , vol.50 , pp. 6507-6518
    • Nabuurs, S.B.1    Wagener, M.2    De Vlieg, J.3
  • 91
    • 0036882099 scopus 로고    scopus 로고
    • Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility
    • Kairys, V.; Gilson, M.K. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. J. Comput. Chem. 2002, 23, 1656-1670.
    • (2002) J. Comput. Chem. , vol.23 , pp. 1656-1670
    • Kairys, V.1    Gilson, M.K.2
  • 92
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A.R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 1994, 235, 345-356.
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 93
    • 0037379786 scopus 로고    scopus 로고
    • Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities
    • Frimurer, T.M.; Peters, G.H.; Iversen, L.F.; Andersen, H.S.; Moller, N.P.; Olsen, O.H. Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. Biophys. J. 2003, 84, 2273-2281.
    • (2003) Biophys. J. , vol.84 , pp. 2273-2281
    • Frimurer, T.M.1    Peters, G.H.2    Iversen, L.F.3    Andersen, H.S.4    Moller, N.P.5    Olsen, O.H.6
  • 94
    • 59849126340 scopus 로고    scopus 로고
    • Docking and scoring with alternative side-chain conformations
    • Hartmann, C.; Antes, I.; Lengauer, T. Docking and scoring with alternative side-chain conformations. Proteins 2009, 74, 712-726.
    • (2009) Proteins , vol.74 , pp. 712-726
    • Hartmann, C.1    Antes, I.2    Lengauer, T.3
  • 95
    • 0032190489 scopus 로고    scopus 로고
    • Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
    • Schnecke, V.; Swanson, C.A.; Getzoff, E.D.; Tainer, J.A.; Kuhn, L.A. Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 1998, 33, 74-87.
    • (1998) Proteins , vol.33 , pp. 74-87
    • Schnecke, V.1    Swanson, C.A.2    Getzoff, E.D.3    Tainer, J.A.4    Kuhn, L.A.5
  • 96
    • 15244353539 scopus 로고    scopus 로고
    • Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis
    • Zavodszky, M.I.; Kuhn, L.A. Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci. 2005, 14, 1104-1114.
    • (2005) Protein Sci. , vol.14 , pp. 1104-1114
    • Zavodszky, M.I.1    Kuhn, L.A.2
  • 98
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs, D.J.; Rader, A.J.; Kuhn, L.A.; Thorpe, M.F. Protein flexibility predictions using graph theory. Proteins 2001, 44, 150-165.
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 99
    • 4544310320 scopus 로고    scopus 로고
    • Modeling correlated main-chain motions in proteins for flexible molecular recognition
    • Zavodszky, M.I.; Lei, M.; Thorpe, M.F.; Day, A.R.; Kuhn, L.A. Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins 2004, 57, 243-261.
    • (2004) Proteins , vol.57 , pp. 243-261
    • Zavodszky, M.I.1    Lei, M.2    Thorpe, M.F.3    Day, A.R.4    Kuhn, L.A.5
  • 100
    • 36749008588 scopus 로고    scopus 로고
    • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    • Arora, K.; Brooks, C.L., 3rd. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc. Natl. Acad. Sci. U S A 2007, 104, 18496-18501.
    • (2007) Proc. Natl. Acad. Sci. U S A , vol.104 , pp. 18496-18501
    • Arora, K.1    Brooks, C.L.2
  • 101
    • 0037231646 scopus 로고    scopus 로고
    • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    • Lin, J.H.; Perryman, A.L.; Schames, J.R.; McCammon, J.A. The relaxed complex method: Accommodating receptor flexibility for drug 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
  • 102
    • 50249114683 scopus 로고    scopus 로고
    • An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
    • Amaro, R.E.; Baron, R.; McCammon, J.A. An improved relaxed complex 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
  • 103
    • 35548942306 scopus 로고    scopus 로고
    • Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models
    • Bowman, A.L.; Nikolovska-Coleska, Z.; Zhong, H.; Wang, S.; Carlson, H.A. Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. J. Am. Chem. Soc. 2007, 129, 12809-12814.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 12809-12814
    • Bowman, A.L.1    Nikolovska-coleska, Z.2    Zhong, H.3    Wang, S.4    Carlson, H.A.5
  • 104
    • 34447271743 scopus 로고    scopus 로고
    • Exploring experimental sources of multiple protein conformations in structure-based drug design
    • Damm, K.L.; Carlson, H.A. Exploring experimental sources of multiple protein conformations in structure-based drug design. J. Am. Chem. Soc. 2007, 129, 8225-8235.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 8225-8235
    • Damm, K.L.1    Carlson, H.A.2
  • 106
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking
    • Huang, S.Y.; Zou, X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 2007, 66, 399-421.
    • (2007) Proteins , vol.66 , pp. 399-421
    • Huang, S.Y.1    Zou, X.2
  • 107
    • 33845923184 scopus 로고    scopus 로고
    • Efficient molecular docking of NMR structures: application to HIV-1 protease
    • Huang, S.Y.; Zou, X. Efficient molecular docking of NMR structures: application to HIV-1 protease. Protein Sci. 2007, 16, 43-51.
    • (2007) Protein Sci. , vol.16 , pp. 43-51
    • Huang, S.Y.1    Zou, X.2
  • 108
    • 57349156167 scopus 로고    scopus 로고
    • In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking
    • Bolstad, E.S.; Anderson, A.C. In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking. Proteins 2008, 73, 566-580.
    • (2008) Proteins , vol.73 , pp. 566-580
    • Bolstad, E.S.1    Anderson, A.C.2
  • 109
    • 55749100817 scopus 로고    scopus 로고
    • Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations
    • Durdagi, S.; Mavromoustakos, T.; Chronakis, N.; Papadopoulos, M. G. Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations. Bioorg. Med. Chem. 2008, 16, 9957-9974.
    • (2008) Bioorg. Med. Chem. , vol.16 , pp. 9957-9974
    • Durdagi, S.1    Mavromoustakos, T.2    Chronakis, N.3    Papadopoulos, M.G.4
  • 110
    • 0034465217 scopus 로고    scopus 로고
    • A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening
    • Broughton, H.B. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. J. Mol. Graph. Model. 2000, 18, 247-257.
    • (2000) , vol.18 , pp. 247-257
    • Broughton, H.B.1
  • 111
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg, F.; Morris, G.M.; Sanner, M.F.; Olson, A.J.; Goodsell, D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002, 46, 34-40.
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 112
    • 65249157200 scopus 로고    scopus 로고
    • In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking
    • Bolstad, E.S.; Anderson, A.C. In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking. Proteins 2009, 75, 62-74.
    • (2009) Proteins , vol.75 , pp. 62-74
    • Bolstad, E.S.1    Anderson, A.C.2
  • 113
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: efficient molecular docking considering protein structure variations
    • Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: efficient molecular 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
  • 114
    • 60549086155 scopus 로고    scopus 로고
    • Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking
    • Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J. Med. Chem. 2009, 52, 397-406.
    • (2009) J. Med. Chem. , vol.52 , pp. 397-406
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 115
    • 33749004010 scopus 로고    scopus 로고
    • How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding
    • Thorsteinsdottir, H.B.; Schwede, T.; Zoete, V.; Meuwly, M. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding. Proteins 2006, 65, 407-423.
    • (2006) Proteins , vol.65 , pp. 407-423
    • Thorsteinsdottir, H.B.1    Schwede, T.2    Zoete, V.3    Meuwly, M.4
  • 116
    • 61449209190 scopus 로고    scopus 로고
    • Experimental approaches to evaluate the thermodynamics of protein-drug interactions
    • de Azevedo, W.F., Jr.; Dias, R. Experimental approaches to evaluate the thermodynamics of protein-drug interactions. Curr. Drug Targets 2008, 9, 1071-1076.
    • (2008) Curr. Drug Targets , vol.9 , pp. 1071-1076
    • De Azevedo Jr, W.F.1    Dias, R.2
  • 117
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu, T.; Lin, Y.; Wen, X.; Jorissen, R.N.; Gilson, M.K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007, 35, D198-201.
    • (2007) Nucleic Acids Res. , vol.35
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 118
    • 60349109713 scopus 로고    scopus 로고
    • Computational evaluation of protein-small molecule binding
    • Guvench, O.; MacKerell, A.D., Jr. Computational evaluation of protein-small molecule binding. Curr. Opin. Struct. Biol. 2009, 19, 56-61.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 56-61
    • Guvench, O.1    MacKerell Jr, A.D.2
  • 119
    • 64049102289 scopus 로고    scopus 로고
    • Binding of small-molecule ligands to proteins: "what you see" is not always "what you get"
    • Mobley, D.L.; Dill, K.A. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure 2009, 17, 489-498.
    • (2009) Structure , vol.17 , pp. 489-498
    • Mobley, D.L.1    Dill, K.A.2
  • 121
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding free energy from computer simulations
    • Woo, H.J.; Roux, B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc. Natl. Acad. Sci. U S A 2005, 102, 6825-6830.
    • (2005) Proc. Natl. Acad. Sci. U S A , vol.102 , pp. 6825-6830
    • Woo, H.J.1    Roux, B.2
  • 122
    • 65249154272 scopus 로고    scopus 로고
    • Standard free energy of binding from a one-dimensional potential of mean force
    • Doudou, S.; Burton, N.A.; Henchman, R.H. Standard free energy of binding from a one-dimensional potential of mean force. J. Chem. Theory Comput. 2009, 5, 909-918.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 909-918
    • Doudou, S.1    Burton, N.A.2    Henchman, R.H.3
  • 123
    • 0000299809 scopus 로고
    • Aromatic-aromatic interactions: free-energy profiles for the benzene dimer in water, chloroform, and liquid benzene
    • Jorgensen, W.L.; Severance, D.L. Aromatic-aromatic interactions: free-energy profiles for the benzene dimer in water, chloroform, and liquid benzene. J. Am. Chem. Soc. 1990, 112, 4768-4774.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 4768-4774
    • Jorgensen, W.L.1    Severance, D.L.2
  • 124
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux, B. The calculation of the potential of mean force using computer simulations. Comp. Phys. Comm. 1995, 91, 275-282.
    • (1995) Comp. Phys. Comm. , vol.91 , pp. 275-282
    • Roux, B.1
  • 125
    • 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
  • 126
    • 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
  • 127
    • 23744478437 scopus 로고    scopus 로고
    • Free energy surfaces from single-molecule force spectroscopy
    • Hummer, G.; Szabo, A. Free energy surfaces from single-molecule force spectroscopy. Acc. Chem. Res. 2005, 38, 504-513.
    • (2005) Acc. Chem. Res. , vol.38 , pp. 504-513
    • Hummer, G.1    Szabo, A.2
  • 130
    • 67650087533 scopus 로고    scopus 로고
    • Validating charmm parameters and exploring charge distribution rules in structure-based drug design
    • Knight, J.L.; Brooks, C.L. Validating charmm parameters and exploring charge distribution rules in structure-based drug design. Journal of Chemical Theory and Computation 2009, 5, 1680-1691.
    • (2009) Journal of Chemical Theory and Computation , vol.5 , pp. 1680-1691
    • Knight, J.L.1    Brooks, C.L.2
  • 131
    • 33845290650 scopus 로고    scopus 로고
    • FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase
    • Kim, J.T.; Hamilton, A.D.; Bailey, C.M.; Domaoal, R.A.; Wang, L.; Anderson, K.S.; Jorgensen, W L. FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase. J. Am. Chem. Soc. 2006, 128, 15372-15373.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 15372-15373
    • Kim, J.T.1    Hamilton, A.D.2    Bailey, C.M.3    Domaoal, R.A.4    Wang, L.5    Anderson, K.S.6    Jorgensen, W.L.7
  • 132
    • 56249130101 scopus 로고    scopus 로고
    • Michel, J.; Essex, J.W. Hit identification and binding mode predictions by rigorous free energy simulations. J. Med. Chem. 2008, 51, 6654-6664.
    • (2008) J. Med. Chem. , vol.51 , pp. 6654-6664
    • Michel, J.1    Essex, J.W.2
  • 133
    • 2342648012 scopus 로고    scopus 로고
    • Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions
    • Blondel, A. Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions. J. Comput. Chem. 2004, 25, 985-993.
    • (2004) J. Comput. Chem. , vol.25 , pp. 985-993
    • Blondel, A.1
  • 134
    • 70349466388 scopus 로고    scopus 로고
    • Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data
    • Shyu, C.; Ytreberg, F.M. Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data. J. Comput. Chem. 2009, 30, 2297-2304.
    • (2009) J. Comput. Chem. , vol.30 , pp. 2297-2304
    • Shyu, C.1    Ytreberg, F.M.2
  • 136
    • 70449522914 scopus 로고    scopus 로고
    • Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site
    • Boyce, S.E.; Mobley, D.L.; Rocklin, G.J.; Graves, A.P.; Dill, K.A.; Shoichet, B.K. Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site. J. Mol. Biol. 2009, 394, 747-763.
    • (2009) J. Mol. Biol. , vol.394 , pp. 747-763
    • Boyce, S.E.1    Mobley, D.L.2    Rocklin, G.J.3    Graves, A.P.4    Dill, K.A.5    Shoichet, B.K.6
  • 137
  • 138
    • 3042549928 scopus 로고    scopus 로고
    • Binding affinity prediction with different force fields: examination of the linear interaction energy method
    • Almlöf, M.; Brandsdal, B.O.; Aqvist, J. Binding affinity prediction with different force fields: examination of the linear interaction energy method. J. Comput. Chem. 2004, 25, 1242-1254.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1242-1254
    • Almlöf, M.1    Brandsdal, B.O.2    Aqvist, J.3
  • 139
    • 67349091039 scopus 로고    scopus 로고
    • Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity
    • Alam, M.A.; Naik, P.K. Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity. Journal of Molecular Graphics & Modelling 2009, 27, 930-943.
    • (2009) Journal of Molecular Graphics & Modelling , vol.27 , pp. 930-943
    • Alam, M.A.1    Naik, P.K.2
  • 140
    • 68149091436 scopus 로고    scopus 로고
    • alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases
    • Orrling, K.M.; Marzahn, M.R.; Gutierrez-de-Teran, H.; Aqvist, J.; Dunn, B.M.; Larhed, M. alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases. Bioorg. Med. Chem. 2009, 17, 5933-5949.
    • (2009) Bioorg. Med. Chem. , vol.17 , pp. 5933-5949
    • Orrling, K.M.1    Marzahn, M.R.2    Gutierrez-de-teran, H.3    Aqvist, J.4    Dunn, B.M.5    Larhed, M.6
  • 141
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices
    • Srinivasan, J.; Cheatham, T.E.; Cieplak, P.; Kollman, P.A.; Case, D.A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 1998, 120, 9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 142
    • 0036677555 scopus 로고    scopus 로고
    • On the calculation of absolute macromolecular binding free energies
    • Luo, H.; Sharp, K. On the calculation of absolute macromolecular binding free energies. Proc. Natl. Acad. Sci. U S A 2002, 99, 10399-10404.
    • (2002) Proc. Natl. Acad. Sci. U S A , vol.99 , pp. 10399-10404
    • Luo, H.1    Sharp, K.2
  • 143
    • 65249187243 scopus 로고    scopus 로고
    • MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface
    • Wong, S.; Amaro, R.E.; McCammon, J.A. MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. J. Chem. Theory Comput. 2009, 5, 422-429.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 422-429
    • Wong, S.1    Amaro, R.E.2    McCammon, J.A.3
  • 144
  • 145
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy
    • Swanson, J.M.; Henchman, R.H.; McCammon, J.A. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 2004, 86, 67-74.
    • (2004) Biophys. J. , vol.86 , pp. 67-74
    • Swanson, J.M.1    Henchman, R.H.2    McCammon, J.A.3
  • 146
    • 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, 238-250.
    • (2004) J. Comput. Chem. , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 147
    • 70350315092 scopus 로고    scopus 로고
    • Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization
    • Michel, J.; Tirado-Rives, J.; Jorgensen, W.L. Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization. J. Am. Chem. Soc. 2009, 131, 15403-15411.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 15403-15411
    • Michel, J.1    Tirado-rives, J.2    Jorgensen, W.L.3
  • 148
    • 41049115037 scopus 로고    scopus 로고
    • Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
    • Deng, Y.; Roux, B. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. J. Chem. Phys. 2008, 128, 115103.
    • (2008) J. Chem. Phys. , vol.128 , pp. 115103
    • Deng, Y.1    Roux, B.2
  • 149
    • 67650077383 scopus 로고    scopus 로고
    • Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results
    • ten Brink, T.; Exner, T.E. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J. Chem. Inf. Model. 2009, 49, 1535-1546.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1535-1546
    • Ten Brink, T.1    Exner, T.E.2
  • 150
    • 65549146701 scopus 로고    scopus 로고
    • Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT
    • Ritschel, T.; Hoertner, S.; Heine, A.; Diederich, F.; Klebe, G. Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT. Chembiochem 2009, 10, 716-727.
    • (2009) Chembiochem , vol.10 , pp. 716-727
    • Ritschel, T.1    Hoertner, S.2    Heine, A.3    Diederich, F.4    Klebe, G.5
  • 151
    • 44049091290 scopus 로고    scopus 로고
    • Calculation of protein-ligand binding free energy by using a polarizable potential
    • Jiao, D.; Golubkov, P.A.; Darden, T.A.; Ren, P. Calculation of protein-ligand binding free energy by using a polarizable potential. Proc. Natl. Acad. Sci. U S A 2008, 105, 6290-6295.
    • (2008) Proc. Natl. Acad. Sci. U S A , vol.105 , pp. 6290-6295
    • Jiao, D.1    Golubkov, P.A.2    Darden, T.A.3    Ren, P.4
  • 154
    • 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
  • 155
    • 40749134545 scopus 로고    scopus 로고
    • Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A
    • Tang, J.; Park, J.G.; Millard, C.B.; Schmidt, J.J.; Pang, Y.P. Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A. PLoS One 2007, 2, e761.
    • (2007) PLoS One , vol.2
    • Tang, J.1    Park, J.G.2    Millard, C.B.3    Schmidt, J.J.4    Pang, Y.P.5
  • 156
    • 34548141774 scopus 로고    scopus 로고
    • Targeting plague virulence factors: a combined machine learning method and multiple conformational virtual screening for the discovery of Yersinia protein kinase A inhibitors
    • Hu, X.; Prehna, G.; Stebbins, C.E. Targeting plague virulence factors: a combined machine learning method and multiple conformational virtual screening for the discovery of Yersinia protein kinase A inhibitors. J. Med. Chem. 2007, 50, 3980-3983.
    • (2007) J. Med. Chem. , vol.50 , pp. 3980-3983
    • Hu, X.1    Prehna, G.2    Stebbins, C.E.3
  • 158
    • 57349106476 scopus 로고    scopus 로고
    • Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking
    • Hritz, J.; de Ruiter, A.; Oostenbrink, C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking. J. Med. Chem. 2008, 51, 7469-7477.
    • (2008) J. Med. Chem. , vol.51 , pp. 7469-7477
    • Hritz, J.1    De Ruiter, A.2    Oostenbrink, C.3


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