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Volumn 17, Issue 4, 2009, Pages 489-498

Binding of Small-Molecule Ligands to Proteins: "What You See" Is Not Always "What You Get"

Author keywords

PROTEINS

Indexed keywords

ION; LIGAND; PROTEIN; RECEPTOR; WATER;

EID: 64049102289     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2009.02.010     Document Type: Review
Times cited : (467)

References (148)
  • 1
    • 40949163431 scopus 로고    scopus 로고
    • Role of the active-site solvent thermodynamics of factor Xa ligand binding
    • Abel R., Young T., Farid R., Berne B.J., and Friesner R.A. Role of the active-site solvent thermodynamics of factor Xa ligand binding. J. Am. Chem. Soc. 130 (2008) 2817-2831
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 2817-2831
    • Abel, R.1    Young, T.2    Farid, R.3    Berne, B.J.4    Friesner, R.A.5
  • 2
    • 36749008588 scopus 로고    scopus 로고
    • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    • Arora K., and Brooks III C.L. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 18496-18501
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 18496-18501
    • Arora, K.1    Brooks III, C.L.2
  • 5
    • 33847655150 scopus 로고    scopus 로고
    • Classification of water molecules in protein binding sites
    • Barillari C., Taylor J., Viner R., and Essex J.W. Classification of water molecules in protein binding sites. J. Am. Chem. Soc. 129 (2007) 2577-2587
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 2577-2587
    • Barillari, C.1    Taylor, J.2    Viner, R.3    Essex, J.W.4
  • 6
    • 0023106632 scopus 로고
    • Calculation of the relative change in binding free energy of a protein-inhibitor complex
    • Bash P.A., Singh U.C., Brown F.K., Langridge R., and Kollman P.A. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 235 (1987) 574-576
    • (1987) Science , vol.235 , pp. 574-576
    • Bash, P.A.1    Singh, U.C.2    Brown, F.K.3    Langridge, R.4    Kollman, P.A.5
  • 7
    • 0024498518 scopus 로고
    • Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding
    • Birdsall B., Feeney J., Tendler S.J.B., Hammond S.J., and Roberts G.C.K. Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding. Biochemistry 28 (1989) 2297-2305
    • (1989) Biochemistry , vol.28 , pp. 2297-2305
    • Birdsall, B.1    Feeney, J.2    Tendler, S.J.B.3    Hammond, S.J.4    Roberts, G.C.K.5
  • 8
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr D.D., McElheny D., Dyson H.J., and Wright P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313 (2006) 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 9
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm H.J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8 (1993) 243-256
    • (1993) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 10
    • 0030474049 scopus 로고    scopus 로고
    • What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?
    • Böhm H.J., and Klebe G. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?. Angew. Chem. Int. Ed. Engl. 35 (1996) 2588-2614
    • (1996) Angew. Chem. Int. Ed. Engl. , vol.35 , pp. 2588-2614
    • Böhm, H.J.1    Klebe, G.2
  • 11
    • 0141682863 scopus 로고    scopus 로고
    • Absolute binding free energies: a quantitative approach for their calculation
    • Boresch S., Tettinger F., Leitgeb M., and Karplus M. Absolute binding free energies: a quantitative approach for their calculation. J. Phys. Chem. A 107 (2003) 9535-9551
    • (2003) J. Phys. Chem. A , vol.107 , pp. 9535-9551
    • Boresch, S.1    Tettinger, F.2    Leitgeb, M.3    Karplus, M.4
  • 12
    • 33750981540 scopus 로고    scopus 로고
    • Do structurally similar ligands bind in a similar fashion?
    • Bostrom J., Hogner A., and Schmitt S. Do structurally similar ligands bind in a similar fashion?. J. Med. Chem. 49 (2006) 6716-6725
    • (2006) J. Med. Chem. , vol.49 , pp. 6716-6725
    • Bostrom, J.1    Hogner, A.2    Schmitt, S.3
  • 14
    • 5644287368 scopus 로고    scopus 로고
    • Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm
    • Chang C.E., and Gilson M.K. Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. J. Am. Chem. Soc. 126 (2004) 13156-13164
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 13156-13164
    • Chang, C.E.1    Gilson, M.K.2
  • 16
    • 0008589609 scopus 로고    scopus 로고
    • Recent successes and continuing limitations in computer aided drug design
    • Charifson P.S. (Ed), Dekker, New York
    • Charifson P.S., and Kuntz I.D. Recent successes and continuing limitations in computer aided drug design. In: Charifson P.S. (Ed). Practical Application of Computer Aided Drug Design (1997), Dekker, New York
    • (1997) Practical Application of Computer Aided Drug Design
    • Charifson, P.S.1    Kuntz, I.D.2
  • 17
    • 0031788539 scopus 로고    scopus 로고
    • Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
    • Cheatham T.E., Srinivasan J., Case D.A., and Kollman P.A. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 16 (1998) 265-280
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 265-280
    • Cheatham, T.E.1    Srinivasan, J.2    Case, D.A.3    Kollman, P.A.4
  • 18
    • 16344395749 scopus 로고    scopus 로고
    • Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design
    • Chen W., Chang C.E., and Gilson M.K. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys. J. 87 (2004) 3035-3049
    • (2004) Biophys. J. , vol.87 , pp. 3035-3049
    • Chen, W.1    Chang, C.E.2    Gilson, M.K.3
  • 19
    • 33644955487 scopus 로고    scopus 로고
    • The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution
    • Chen Y., Minasov G., Roth T.A., Prati F., and Shoichet B.K. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J. Am. Chem. Soc. 128 (2006) 2970-2976
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2970-2976
    • Chen, Y.1    Minasov, G.2    Roth, T.A.3    Prati, F.4    Shoichet, B.K.5
  • 20
    • 0034835794 scopus 로고    scopus 로고
    • Protein side-chain rotamers from dipolar couplings in a liquid crystalline phase
    • Chou J.J., and Bax A. Protein side-chain rotamers from dipolar couplings in a liquid crystalline phase. J. Am. Chem. Soc. 123 (2001) 3844-3845
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 3844-3845
    • Chou, J.J.1    Bax, A.2
  • 21
    • 53549089920 scopus 로고    scopus 로고
    • Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects
    • Constantine K.L., Mueller L., Metzler W.J., McDonnell P.A., Todderud G., Goldfarb V., Fan Y., Newitt J.A., Keifer S.E., Gao M., et al. Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects. J. Med. Chem. 51 (2008) 6225-6229
    • (2008) J. Med. Chem. , vol.51 , pp. 6225-6229
    • Constantine, K.L.1    Mueller, L.2    Metzler, W.J.3    McDonnell, P.A.4    Todderud, G.5    Goldfarb, V.6    Fan, Y.7    Newitt, J.A.8    Keifer, S.E.9    Gao, M.10
  • 22
    • 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., and Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J. Chem. Inf. Model. 47 (2007) 435-449
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 435-449
    • Corbeil, C.R.1    Englebienne, P.2    Moitessier, N.3
  • 24
    • 34547657456 scopus 로고    scopus 로고
    • Atypical protonation states in the active site of HIV-1 protease: a computational study
    • Czodrowski P., Sotriffer C.A., and Klebe G. Atypical protonation states in the active site of HIV-1 protease: a computational study. J. Chem. Inf. Model. 47 (2007) 1590-1598
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1590-1598
    • Czodrowski, P.1    Sotriffer, C.A.2    Klebe, G.3
  • 25
    • 33749238080 scopus 로고    scopus 로고
    • Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant
    • Deng Y., and Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J. Chem. Theory Comput. 2 (2006) 1255-1273
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 1255-1273
    • Deng, Y.1    Roux, B.2
  • 26
    • 0035799367 scopus 로고    scopus 로고
    • Dynamics of protein ligand binding on multiple time scales: NADH binding to lactate dehydrogenase
    • Deng H., Zhadin N., and Callender R. Dynamics of protein ligand binding on multiple time scales: NADH binding to lactate dehydrogenase. Biochemistry 40 (2001) 3767-3773
    • (2001) Biochemistry , vol.40 , pp. 3767-3773
    • Deng, H.1    Zhadin, N.2    Callender, R.3
  • 27
    • 0035955550 scopus 로고    scopus 로고
    • Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition
    • Dullweber F., Stubbs M.T., Musil D., Sturzebecher J., and Klebe G. Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. J. Mol. Biol. 313 (2001) 593-614
    • (2001) J. Mol. Biol. , vol.313 , pp. 593-614
    • Dullweber, F.1    Stubbs, M.T.2    Musil, D.3    Sturzebecher, J.4    Klebe, G.5
  • 31
    • 33846230547 scopus 로고    scopus 로고
    • "Four-dimensional" protein structures: examples from metalloproteins
    • Fragai M., Luchinat C., and Parigi G. "Four-dimensional" protein structures: examples from metalloproteins. Acc. Chem. Res. 39 (2006) 909-917
    • (2006) Acc. Chem. Res. , vol.39 , pp. 909-917
    • Fragai, M.1    Luchinat, C.2    Parigi, G.3
  • 35
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M., Lesk A.M., and Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 33 (1994) 6739-6749
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 37
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke H., and Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed. 41 (2002) 2645-2676
    • (2002) Angew. Chem. Int. Ed. , vol.41 , pp. 2645-2676
    • Gohlke, H.1    Klebe, G.2
  • 40
    • 0028297112 scopus 로고
    • Application of the three-dimensional structures of protein target molecules in structure-based drug design
    • Greer J., Erickson J.W., Baldwin J.J., and Varney M.D. Application of the three-dimensional structures of protein target molecules in structure-based drug design. J. Med. Chem. 37 (1994) 1035-1047
    • (1994) J. Med. Chem. , vol.37 , pp. 1035-1047
    • Greer, J.1    Erickson, J.W.2    Baldwin, J.J.3    Varney, M.D.4
  • 41
    • 45749138489 scopus 로고    scopus 로고
    • MM-GB/SA rescoring of docking poses in structure-based lead optimization
    • Guimaraes C.R.W., and Cardozo M. MM-GB/SA rescoring of docking poses in structure-based lead optimization. J. Chem. Inf. Model. 48 (2008) 958-970
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 958-970
    • Guimaraes, C.R.W.1    Cardozo, M.2
  • 42
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • Gutteridge A., and Thornton J. Conformational changes observed in enzyme crystal structures upon substrate binding. J. Mol. Biol. 346 (2005) 21-28
    • (2005) J. Mol. Biol. , vol.346 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 43
    • 2942659093 scopus 로고    scopus 로고
    • Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method
    • Hamelberg D., and McCammon J.A. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J. Am. Chem. Soc. 126 (2004) 7683-7689
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 7683-7689
    • Hamelberg, D.1    McCammon, J.A.2
  • 44
    • 37249023634 scopus 로고    scopus 로고
    • Torsion angle preference and energetics of small-molecule ligands bound to proteins
    • Hao M.H., Haq O., and Muegge I. Torsion angle preference and energetics of small-molecule ligands bound to proteins. J. Chem. Inf. Model. 47 (2007) 2242-2252
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 2242-2252
    • Hao, M.H.1    Haq, O.2    Muegge, I.3
  • 46
    • 0031079364 scopus 로고    scopus 로고
    • "Mining minima": direct computation of conformational free energy
    • Head M.S., Given J.A., and Gilson M.K. "Mining minima": direct computation of conformational free energy. J. Phys. Chem. A 101 (1997) 1609-1618
    • (1997) J. Phys. Chem. A , vol.101 , pp. 1609-1618
    • Head, M.S.1    Given, J.A.2    Gilson, M.K.3
  • 47
    • 0029160249 scopus 로고
    • Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study
    • Helms V., and Wade R.C. Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Biophys. J. 69 (1995) 810-824
    • (1995) Biophys. J. , vol.69 , pp. 810-824
    • Helms, V.1    Wade, R.C.2
  • 48
    • 0032054675 scopus 로고    scopus 로고
    • Computational alchemy to calculate absolute protein-ligand binding free energy
    • Helms V., and Wade R.C. Computational alchemy to calculate absolute protein-ligand binding free energy. J. Am. Chem. Soc. 120 (1998) 2710-2713
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 2710-2713
    • Helms, V.1    Wade, R.C.2
  • 49
    • 0032529586 scopus 로고    scopus 로고
    • Hydration energy landscape of the active site cavity in cytochrome P450cam
    • Helms V., and Wade R.C. Hydration energy landscape of the active site cavity in cytochrome P450cam. Proteins Struct. Funct. Genet. 32 (1998) 381-396
    • (1998) Proteins Struct. Funct. Genet. , vol.32 , pp. 381-396
    • Helms, V.1    Wade, R.C.2
  • 50
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman K., and Kern D. Dynamic personalities of proteins. Nature 450 (2007) 964-972
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 52
    • 85005687495 scopus 로고
    • The free energy of xenon binding to myoglobin from molecular dynamics simulation
    • Hermans J., and Subramaniam S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr. J. Chem. 27 (1986) 225-227
    • (1986) Isr. J. Chem. , vol.27 , pp. 225-227
    • Hermans, J.1    Subramaniam, S.2
  • 53
    • 0030887944 scopus 로고    scopus 로고
    • Inclusion of the loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
    • Hermans J., and Wang L. Inclusion of the loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J. Am. Chem. Soc. 119 (1997) 2707-2714
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 2707-2714
    • Hermans, J.1    Wang, L.2
  • 54
    • 34347235156 scopus 로고    scopus 로고
    • Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins
    • Hilser V.J., and Thompson E.B. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 8311-8315
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 8311-8315
    • Hilser, V.J.1    Thompson, E.B.2
  • 55
    • 34249040810 scopus 로고    scopus 로고
    • Physics-based methods for studying protein-ligand interactions
    • Huang N., and Jacobson M.P. Physics-based methods for studying protein-ligand interactions. Curr. Opin. Drug Discov. Dev. 10 (2007) 325-331
    • (2007) Curr. Opin. Drug Discov. Dev. , vol.10 , pp. 325-331
    • Huang, N.1    Jacobson, M.P.2
  • 57
    • 33947716119 scopus 로고    scopus 로고
    • A semiempirical free energy force field with charge-based desolvation
    • Huey R., Morris G.M., Olson A.J., and Goodsell D.S. A semiempirical free energy force field with charge-based desolvation. J. Comput. Chem. 28 (2007) 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
    • 0037187412 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design
    • Huo S., Wang J., Cieplak P., Kollman P.A., and Kuntz I.D. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J. Med. Chem. 45 (2002) 1412-1419
    • (2002) J. Med. Chem. , vol.45 , pp. 1412-1419
    • Huo, S.1    Wang, J.2    Cieplak, P.3    Kollman, P.A.4    Kuntz, I.D.5
  • 59
    • 33748267063 scopus 로고    scopus 로고
    • Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
    • Jayachandran G., Shirts M.R., Park S., and Pande V.S. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J. Chem. Phys. 125 (2006) 084901
    • (2006) J. Chem. Phys. , vol.125 , pp. 084901
    • Jayachandran, G.1    Shirts, M.R.2    Park, S.3    Pande, V.S.4
  • 60
    • 44049091290 scopus 로고    scopus 로고
    • Calculation of protein-ligand binding free energy using a polarizable potential
    • Jiao D., Golubkov P.A., Darden T.A., and Ren P. Calculation of protein-ligand binding free energy using a polarizable potential. Proc. Nat. Acad. Sci U.S.A. 105 (2008) 6290-6295
    • (2008) Proc. Nat. Acad. Sci U.S.A. , vol.105 , pp. 6290-6295
    • Jiao, D.1    Golubkov, P.A.2    Darden, T.A.3    Ren, P.4
  • 61
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen W.L. The many roles of computation in drug discovery. Science 303 (2004) 1813-1818
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 62
    • 0034824313 scopus 로고    scopus 로고
    • Electrostatic complementarity at ligand binding sites: application to chorismate mutase
    • Kangas E., and Tidor B. Electrostatic complementarity at ligand binding sites: application to chorismate mutase. J. Phys. Chem. B 105 (2001) 880-888
    • (2001) J. Phys. Chem. B , vol.105 , pp. 880-888
    • Kangas, E.1    Tidor, B.2
  • 63
    • 34548785534 scopus 로고    scopus 로고
    • Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
    • Kim K.H. Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?. J. Comput. Aided Mol. Des. 21 (2007) 421-435
    • (2007) J. Comput. Aided Mol. Des. , vol.21 , pp. 421-435
    • Kim, K.H.1
  • 64
    • 33947195392 scopus 로고    scopus 로고
    • Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?
    • Kim K.H. Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?. J. Comput. Aided Mol. Des. 21 (2007) 63-86
    • (2007) J. Comput. Aided Mol. Des. , vol.21 , pp. 63-86
    • Kim, K.H.1
  • 65
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
    • Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33 (2000) 889-897
    • (2000) Acc. Chem. Res. , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10
  • 66
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • Kuhn B., and Kollman P.A. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 43 (2000) 3786-3791
    • (2000) J. Med. Chem. , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 68
    • 0141990820 scopus 로고    scopus 로고
    • Specific empirical free energy function for automated docking of carbohydrates to proteins
    • Laederach A., and Reilly P.J. Specific empirical free energy function for automated docking of carbohydrates to proteins. J. Comput. Chem. 24 (2003) 1748-1757
    • (2003) J. Comput. Chem. , vol.24 , pp. 1748-1757
    • Laederach, A.1    Reilly, P.J.2
  • 69
    • 0028206116 scopus 로고
    • X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites
    • LaLonde J.M., Bernlohr D.A., and Banaszak L.J. X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites. Biochemistry 33 (1994) 4885-4895
    • (1994) Biochemistry , vol.33 , pp. 4885-4895
    • LaLonde, J.M.1    Bernlohr, D.A.2    Banaszak, L.J.3
  • 70
    • 0036568354 scopus 로고    scopus 로고
    • Contributions to the binding free energy of ligands to avidin and streptavidin
    • Lazaridis T., Matsunov A., and Gandolfo F. Contributions to the binding free energy of ligands to avidin and streptavidin. Proteins 47 (2002) 194-208
    • (2002) Proteins , vol.47 , pp. 194-208
    • Lazaridis, T.1    Matsunov, A.2    Gandolfo, F.3
  • 71
    • 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. 235 (1994) 345-356
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 72
    • 33646178918 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
    • Lee M.S., and Olson M.A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys. J. 90 (2006) 864-877
    • (2006) Biophys. J. , vol.90 , pp. 864-877
    • Lee, M.S.1    Olson, M.A.2
  • 73
    • 0029894436 scopus 로고    scopus 로고
    • Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4
    • Lee H., Reyes V.M., and Kraut J. Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4. Biochemistry 35 (1996) 7012-7020
    • (1996) Biochemistry , vol.35 , pp. 7012-7020
    • Lee, H.1    Reyes, V.M.2    Kraut, J.3
  • 75
    • 33748513468 scopus 로고    scopus 로고
    • Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes
    • Lu Y., Wang C.-Y., and Wang S. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes. J. Am. Chem. Soc. 128 (2006) 11830-11839
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 11830-11839
    • Lu, Y.1    Wang, C.-Y.2    Wang, S.3
  • 76
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations
    • Ma B., Shatsky M., Wolfson H.J., and Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11 (2002) 184-197
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 77
    • 0035367150 scopus 로고    scopus 로고
    • Interpreting trends in the binding of cyclic ureas to HIV-1 protease
    • Mardis K.L., Luo R., and Gilson M.K. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J. Mol. Biol. 309 (2001) 507-517
    • (2001) J. Mol. Biol. , vol.309 , pp. 507-517
    • Mardis, K.L.1    Luo, R.2    Gilson, M.K.3
  • 78
    • 33750056673 scopus 로고    scopus 로고
    • ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
    • Meiler J., and Baker D.A. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65 (2006) 538-548
    • (2006) Proteins , vol.65 , pp. 538-548
    • Meiler, J.1    Baker, D.A.2
  • 80
    • 0030867610 scopus 로고    scopus 로고
    • Ligand binding to proteins: the binding landscape model
    • Miller D.W., and Dill K.A. Ligand binding to proteins: the binding landscape model. Protein Sci. 6 (1997) 2166-2179
    • (1997) Protein Sci. , vol.6 , pp. 2166-2179
    • Miller, D.W.1    Dill, K.A.2
  • 82
    • 27144465458 scopus 로고    scopus 로고
    • Observation of a power-law memory kernel for fluctuations within a single protein molecule
    • Min W., Luo G., Cherayil B.J., Kou S.C., and Xie X.S. Observation of a power-law memory kernel for fluctuations within a single protein molecule. Phys. Rev. Lett. 94 (2005) 198302
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 198302
    • Min, W.1    Luo, G.2    Cherayil, B.J.3    Kou, S.C.4    Xie, X.S.5
  • 83
    • 33748252631 scopus 로고    scopus 로고
    • On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
    • Mobley D.L., Chodera J.D., and Dill K.A. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J. Chem. Phys. 125 (2006) 084902
    • (2006) J. Chem. Phys. , vol.125 , pp. 084902
    • Mobley, D.L.1    Chodera, J.D.2    Dill, K.A.3
  • 84
    • 36049017659 scopus 로고    scopus 로고
    • Confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change
    • Mobley D.L., Chodera J.D., and Dill K.A. Confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change. J. Chem. Theory Comput. 3 (2007) 1231-1235
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1231-1235
    • Mobley, D.L.1    Chodera, J.D.2    Dill, K.A.3
  • 86
    • 38949212628 scopus 로고    scopus 로고
    • Treating entropy and conformational changes in implicit solvent simulations of small molecules
    • Mobley D.L., Dill K.A., and Chodera J.D. Treating entropy and conformational changes in implicit solvent simulations of small molecules. J. Phys. Chem. B 112 (2008) 938-946
    • (2008) J. Phys. Chem. B , vol.112 , pp. 938-946
    • Mobley, D.L.1    Dill, K.A.2    Chodera, J.D.3
  • 87
    • 0025311258 scopus 로고
    • Structure, multiple site binding, and segmental accomodation in thymidylate synthase on binding dUMP and an anti-folate
    • Montfort W.R., Perry K.M., Fauman E.B., Finer-Moore J.S., Maley G.F., Hardy L., Maley F., and Stroud R.M. Structure, multiple site binding, and segmental accomodation in thymidylate synthase on binding dUMP and an anti-folate. Biochemistry 29 (1990) 6964-6977
    • (1990) Biochemistry , vol.29 , pp. 6964-6977
    • Montfort, W.R.1    Perry, K.M.2    Fauman, E.B.3    Finer-Moore, J.S.4    Maley, G.F.5    Hardy, L.6    Maley, F.7    Stroud, R.M.8
  • 88
    • 0029067489 scopus 로고
    • Specificity of ligand binding in a buried nonpolar cavity of {T4} lysozyme: linkage of dynamics and structural plasticity
    • Morton A., and Matthews B.W. Specificity of ligand binding in a buried nonpolar cavity of {T4} lysozyme: linkage of dynamics and structural plasticity. Biochemistry 34 (1995) 8576-8588
    • (1995) Biochemistry , vol.34 , pp. 8576-8588
    • Morton, A.1    Matthews, B.W.2
  • 89
    • 0026474757 scopus 로고
    • The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
    • Murthy K.H.M., Winborne E.L., Minnich M.D., Culp J.S., and Debouck C. The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations. J. Biol. Chem. 267 (1992) 22770-22778
    • (1992) J. Biol. Chem. , vol.267 , pp. 22770-22778
    • Murthy, K.H.M.1    Winborne, E.L.2    Minnich, M.D.3    Culp, J.S.4    Debouck, C.5
  • 90
    • 0034656949 scopus 로고    scopus 로고
    • Side-chain flexibility in proteins upon ligand binding
    • Najmanovich R., Kuttner J., Sobolev V., and Edelman M. Side-chain flexibility in proteins upon ligand binding. Proteins 39 (2000) 261-268
    • (2000) Proteins , vol.39 , pp. 261-268
    • Najmanovich, R.1    Kuttner, J.2    Sobolev, V.3    Edelman, M.4
  • 91
    • 1642323740 scopus 로고    scopus 로고
    • Protein kinase inhibitors: insights into drug design from structure
    • Noble M.E., Endicott J.A., and Johnson L.N. Protein kinase inhibitors: insights into drug design from structure. Science 303 (2004) 1800-1805
    • (2004) Science , vol.303 , pp. 1800-1805
    • Noble, M.E.1    Endicott, J.A.2    Johnson, L.N.3
  • 92
    • 3042592839 scopus 로고    scopus 로고
    • Hydration free energies and entropies for water in protein interiors
    • Olano L.R., and Rick S.W. Hydration free energies and entropies for water in protein interiors. J. Am. Chem. Soc. 126 (2004) 7991-8000
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 7991-8000
    • Olano, L.R.1    Rick, S.W.2
  • 93
    • 0346458810 scopus 로고    scopus 로고
    • Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
    • Oostenbrink C., and van Gunsteren W.F. Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation. Proteins 54 (2004) 237-246
    • (2004) Proteins , vol.54 , pp. 237-246
    • Oostenbrink, C.1    van Gunsteren, W.F.2
  • 94
    • 0030874393 scopus 로고    scopus 로고
    • Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site
    • Orville A.M., Elango N., Lipscomb J.D., and Ohlendorf D.H. Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site. Biochemistry 36 (1997) 10039-10051
    • (1997) Biochemistry , vol.36 , pp. 10039-10051
    • Orville, A.M.1    Elango, N.2    Lipscomb, J.D.3    Ohlendorf, D.H.4
  • 95
    • 34249027590 scopus 로고    scopus 로고
    • Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor
    • Pan C., Mezei M., Mujtaba S., Muller M., Zeng L., Li J., Wang Z., and Zhou M.M. Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor. J. Med. Chem. 50 (2007) 2285-2288
    • (2007) J. Med. Chem. , vol.50 , pp. 2285-2288
    • Pan, C.1    Mezei, M.2    Mujtaba, S.3    Muller, M.4    Zeng, L.5    Li, J.6    Wang, Z.7    Zhou, M.M.8
  • 96
    • 0026936915 scopus 로고
    • Predicting the product specificity and coupling of cytochrome P450cam
    • Paulsen M.D., and Ornstein R.L. Predicting the product specificity and coupling of cytochrome P450cam. J. Comput. Aided Mol. Des. 6 (1992) 449-460
    • (1992) J. Comput. Aided Mol. Des. , vol.6 , pp. 449-460
    • Paulsen, M.D.1    Ornstein, R.L.2
  • 97
    • 28144441347 scopus 로고    scopus 로고
    • Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
    • Pearlman D.A. Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J. Med. Chem. 48 (2005) 7796-7807
    • (2005) J. Med. Chem. , vol.48 , pp. 7796-7807
    • Pearlman, D.A.1
  • 98
    • 0035846166 scopus 로고    scopus 로고
    • Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
    • Pearlman D.A., and Charifson P.S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J. Med. Chem. 44 (2001) 3417-3423
    • (2001) J. Med. Chem. , vol.44 , pp. 3417-3423
    • Pearlman, D.A.1    Charifson, P.S.2
  • 99
    • 33745148202 scopus 로고    scopus 로고
    • Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors
    • Pei Z., Li X., Longenecker K., Geldern T.W., Wiedeman P.E., Lubben T.H., Zinker B.A., Stewart K., Ballaron S.J., Stashko M.A., Mika A.K., Beno D.W., et al. Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors. J. Med. Chem. 49 (2006) 3520-3535
    • (2006) J. Med. Chem. , vol.49 , pp. 3520-3535
    • Pei, Z.1    Li, X.2    Longenecker, K.3    Geldern, T.W.4    Wiedeman, P.E.5    Lubben, T.H.6    Zinker, B.A.7    Stewart, K.8    Ballaron, S.J.9    Stashko, M.A.10    Mika, A.K.11    Beno, D.W.12
  • 100
    • 2342586724 scopus 로고    scopus 로고
    • Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding
    • Perola E., and Charifson P.S. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J. Med. Chem. 47 (2004) 2499-2510
    • (2004) J. Med. Chem. , vol.47 , pp. 2499-2510
    • Perola, E.1    Charifson, P.S.2
  • 102
    • 0025761693 scopus 로고
    • Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation
    • Raag R., and Poulos T.L. Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation. Biochemistry 30 (1991) 2674-2684
    • (1991) Biochemistry , vol.30 , pp. 2674-2684
    • Raag, R.1    Poulos, T.L.2
  • 104
    • 0034801307 scopus 로고    scopus 로고
    • Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach
    • Reddy M.R., and Erion M.D. Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach. J. Am. Chem. Soc. 123 (2001) 6246-6252
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 6246-6252
    • Reddy, M.R.1    Erion, M.D.2
  • 106
    • 0033606250 scopus 로고    scopus 로고
    • OPLS all-atom model for amines: resolution of the amine hydration problem
    • Rizzo R.C., and Jorgensen W.L. OPLS all-atom model for amines: resolution of the amine hydration problem. J. Am. Chem. Soc. 121 (1999) 4827-4836
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 4827-4836
    • Rizzo, R.C.1    Jorgensen, W.L.2
  • 107
    • 2542586266 scopus 로고    scopus 로고
    • A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations
    • Rizzo R.C., Toba S., and Kuntz I.D. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. J. Med. Chem. 47 (2004) 3065-3074
    • (2004) J. Med. Chem. , vol.47 , pp. 3065-3074
    • Rizzo, R.C.1    Toba, S.2    Kuntz, I.D.3
  • 108
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study
    • Roux B., Nina M., Poms R., and Smith J.C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys. J. 71 (1996) 670-681
    • (1996) Biophys. J. , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Poms, R.3    Smith, J.C.4
  • 109
    • 22844440711 scopus 로고    scopus 로고
    • New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy
    • Ruvinsky A.M., and Kozintsev A.V. New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. J. Comput. Chem. 26 (2005) 1089-1095
    • (2005) J. Comput. Chem. , vol.26 , pp. 1089-1095
    • Ruvinsky, A.M.1    Kozintsev, A.V.2
  • 111
    • 0036722785 scopus 로고    scopus 로고
    • Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
    • Schwarzl S.M., Tschopp T.B., Smith J.C., and Fischer S. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?. J. Comput. Chem. 23 (2002) 1143-1149
    • (2002) J. Comput. Chem. , vol.23 , pp. 1143-1149
    • Schwarzl, S.M.1    Tschopp, T.B.2    Smith, J.C.3    Fischer, S.4
  • 112
    • 64049112859 scopus 로고    scopus 로고
    • Important considerations impacting molecular docking
    • Shoichet B.K., and Alvarez J. (Eds), CRC Press, Boca Raton, FL
    • Sharp K.A. Important considerations impacting molecular docking. In: Shoichet B.K., and Alvarez J. (Eds). Virtual Screening in Drug Discovery (2005), CRC Press, Boca Raton, FL
    • (2005) Virtual Screening in Drug Discovery
    • Sharp, K.A.1
  • 113
  • 114
    • 79958862887 scopus 로고    scopus 로고
    • Free energy calculations in structure-based drug design
    • Merz K.M., Ringe D., and Reynolds C.H. (Eds), Cambridge University Press, Cambridge
    • Shirts M.R., Mobley D.L., and Brown S.P. Free energy calculations in structure-based drug design. In: Merz K.M., Ringe D., and Reynolds C.H. (Eds). Structure Based Drug Discovery (2009), Cambridge University Press, Cambridge
    • (2009) Structure Based Drug Discovery
    • Shirts, M.R.1    Mobley, D.L.2    Brown, S.P.3
  • 115
  • 116
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • Shoichet B.K., Leach A.R., and Kuntz I.D. Ligand solvation in molecular docking. Proteins 34 (1999) 4-16
    • (1999) Proteins , vol.34 , pp. 4-16
    • Shoichet, B.K.1    Leach, A.R.2    Kuntz, I.D.3
  • 118
    • 33748276474 scopus 로고    scopus 로고
    • Protein-ligand docking: current status and future challenges
    • Sousa S.F., Fernandes P.A., and Ramos M.J. Protein-ligand docking: current status and future challenges. Proteins 65 (2006) 15-26
    • (2006) Proteins , vol.65 , pp. 15-26
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 119
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
    • Srinivasan J., Cheatham III T.E., Cieplak P., Kollman P.A., and Case D.A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120 (1998) 9401-9409
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham III, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 121
    • 33645400172 scopus 로고    scopus 로고
    • A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase
    • Steinbrecher T., Case D.A., and Labahn A. A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase. J. Med. Chem. 49 (2006) 1837-1844
    • (2006) J. Med. Chem. , vol.49 , pp. 1837-1844
    • Steinbrecher, T.1    Case, D.A.2    Labahn, A.3
  • 122
    • 35148897726 scopus 로고    scopus 로고
    • Tracing changes in protonation: a prerequisite to binding to aldose reductase
    • Steuber H., Czodrowski P., Sotriffer C.A., and Klebe G. Tracing changes in protonation: a prerequisite to binding to aldose reductase. J. Mol. Biol. 373 (2007) 1305-1320
    • (2007) J. Mol. Biol. , vol.373 , pp. 1305-1320
    • Steuber, H.1    Czodrowski, P.2    Sotriffer, C.A.3    Klebe, G.4
  • 127
    • 35548976322 scopus 로고    scopus 로고
    • Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
    • Tang C., Schweiters C.D., and Clore G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449 (2007) 1078-1082
    • (2007) Nature , vol.449 , pp. 1078-1082
    • Tang, C.1    Schweiters, C.D.2    Clore, G.M.3
  • 129
    • 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. 2 (2003) 527-541
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 130
    • 0021582448 scopus 로고
    • Ligand-receptor interactions
    • Tembe B.L., and McCammon J.A. Ligand-receptor interactions. Comput. Chem. 8 (1984) 281-283
    • (1984) Comput. Chem. , vol.8 , pp. 281-283
    • Tembe, B.L.1    McCammon, J.A.2
  • 131
    • 33748603755 scopus 로고    scopus 로고
    • Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic
    • Thomson J.A., and Perni R.B. Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic. Curr. Opin. Drug Discov. Devel. 9 (2006) 606-617
    • (2006) Curr. Opin. Drug Discov. Devel. , vol.9 , pp. 606-617
    • Thomson, J.A.1    Perni, R.B.2
  • 132
    • 33749242759 scopus 로고    scopus 로고
    • Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
    • Tirado-Rives J., and Jorgensen W.L. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J. Med. Chem. 49 (2006) 5880-5884
    • (2006) J. Med. Chem. , vol.49 , pp. 5880-5884
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 133
    • 0036315480 scopus 로고    scopus 로고
    • Two 1:1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)
    • Uytterhoeven K., Sponer J., and Meervelt L.V. Two 1:1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). Eur. J. Biochem. 269 (2002) 2868-2877
    • (2002) Eur. J. Biochem. , vol.269 , pp. 2868-2877
    • Uytterhoeven, K.1    Sponer, J.2    Meervelt, L.V.3
  • 134
    • 49649108911 scopus 로고    scopus 로고
    • Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib
    • Vajpai N., Strauss A., Cowan-Jacob S.W., Manley P.W., Crzesiek S., and Jahnke W. Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. J. Biol. Chem. 283 (2008) 18292-18302
    • (2008) J. Biol. Chem. , vol.283 , pp. 18292-18302
    • Vajpai, N.1    Strauss, A.2    Cowan-Jacob, S.W.3    Manley, P.W.4    Crzesiek, S.5    Jahnke, W.6
  • 135
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • Volkman B.F., Lipson D., Wemmer D.E., and Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 291 (2001) 2429-2433
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 137
    • 0033003955 scopus 로고    scopus 로고
    • ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
    • Vorobjev Y.N., and Hermans J. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78 (1999) 195-205
    • (1999) Biophys. Chem. , vol.78 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 138
    • 33749532284 scopus 로고    scopus 로고
    • Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials
    • Wang J., Deng Y., and Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys. J. 91 (2006) 2798-2814
    • (2006) Biophys. J. , vol.91 , pp. 2798-2814
    • Wang, J.1    Deng, Y.2    Roux, B.3
  • 141
    • 0023060081 scopus 로고
    • Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process
    • Warshel A., Sussman F., and King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry 25 (1986) 8368-8372
    • (1986) Biochemistry , vol.25 , pp. 8368-8372
    • Warshel, A.1    Sussman, F.2    King, G.3
  • 143
    • 34247470836 scopus 로고    scopus 로고
    • Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia
    • Weisberg E., Manley P.W., Cowan-Jacob S.W., Hochhaus A., and Griffin J.D. Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia. Nat. Rev. Cancer 7 (2007) 345-356
    • (2007) Nat. Rev. Cancer , vol.7 , pp. 345-356
    • Weisberg, E.1    Manley, P.W.2    Cowan-Jacob, S.W.3    Hochhaus, A.4    Griffin, J.D.5
  • 144
    • 0001486087 scopus 로고
    • Dynamics and design of enzymes and inhibitors
    • Wong C.F., and McCammon J.A. Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 108 (1986) 3830-3832
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 3830-3832
    • Wong, C.F.1    McCammon, J.A.2
  • 145
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
    • Wright P.E., and Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293 (1999) 321-331
    • (1999) J. Mol. Biol. , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 147
    • 0029150760 scopus 로고
    • Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
    • Zhang X.J., Wozniak J.A., and Matthews B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250 (1995) 527-552
    • (1995) J. Mol. Biol. , vol.250 , pp. 527-552
    • Zhang, X.J.1    Wozniak, J.A.2    Matthews, B.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.