메뉴 건너뛰기




Volumn 29, Issue 4, 2011, Pages 159-166

Computational design of protein-ligand interfaces: Potential in therapeutic development

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMPUTATIONAL DESIGN; CONFORMATIONAL SPACE; DRUG DEVELOPMENT; FUTURE PROSPECTS; LOW-ENERGY DESIGN; PROTEIN THERAPEUTICS; SCORING FUNCTIONS; SEARCH ALGORITHMS; SMALL MOLECULES; SMALL-MOLECULE BINDINGS; TIGHT BINDING;

EID: 79952707513     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2011.01.002     Document Type: Review
Times cited : (19)

References (83)
  • 1
    • 37749004225 scopus 로고    scopus 로고
    • Protein therapeutics: a summary and pharmacological classification
    • Leader B., et al. Protein therapeutics: a summary and pharmacological classification. Nat. Rev. Drug Discov. 2008, 7:21-39.
    • (2008) Nat. Rev. Drug Discov. , vol.7 , pp. 21-39
    • Leader, B.1
  • 2
    • 70449723296 scopus 로고    scopus 로고
    • Discovery and development of biopharmaceuticals: current issues
    • Strohl W.R., Knight D.M. Discovery and development of biopharmaceuticals: current issues. Curr. Opin. Biotechnol. 2009, 20:668-672.
    • (2009) Curr. Opin. Biotechnol. , vol.20 , pp. 668-672
    • Strohl, W.R.1    Knight, D.M.2
  • 3
    • 70449375361 scopus 로고    scopus 로고
    • What's fueling the biotech engine-2008
    • Aggarwal S. What's fueling the biotech engine-2008. Nat. Biotechnol. 2009, 27:987-993.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 987-993
    • Aggarwal, S.1
  • 4
    • 78651387929 scopus 로고    scopus 로고
    • Antibody-based therapeutics to watch in 2011
    • Reichert J.M. Antibody-based therapeutics to watch in 2011. MAbs 2011, 3:76-98.
    • (2011) MAbs , vol.3 , pp. 76-98
    • Reichert, J.M.1
  • 5
    • 27144511241 scopus 로고    scopus 로고
    • Engineering novel binding proteins from nonimmunoglobulin domains
    • Binz H.K., et al. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 2005, 23:1257-1268.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 1257-1268
    • Binz, H.K.1
  • 6
    • 67649872364 scopus 로고    scopus 로고
    • Engineered protein scaffolds as next-generation antibody therapeutics
    • Gebauer M., Skerra A. Engineered protein scaffolds as next-generation antibody therapeutics. Curr. Opin. Chem. Biol. 2009, 13:245-255.
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 245-255
    • Gebauer, M.1    Skerra, A.2
  • 7
    • 38949210238 scopus 로고    scopus 로고
    • Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement
    • Calhoun J.R., et al. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Structure 2008, 16:210-215.
    • (2008) Structure , vol.16 , pp. 210-215
    • Calhoun, J.R.1
  • 8
    • 58149476770 scopus 로고    scopus 로고
    • OptGraft: a computational procedure for transferring a binding site onto an existing protein scaffold
    • Fazelinia H., et al. OptGraft: a computational procedure for transferring a binding site onto an existing protein scaffold. Protein Sci. 2009, 18:180-195.
    • (2009) Protein Sci. , vol.18 , pp. 180-195
    • Fazelinia, H.1
  • 9
    • 77949854939 scopus 로고    scopus 로고
    • Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore
    • Fry H.C., et al. Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore. J. Am. Chem. Soc. 2010, 132:3997-4005.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 3997-4005
    • Fry, H.C.1
  • 10
    • 77949327063 scopus 로고    scopus 로고
    • Computational design of second-site suppressor mutations at protein-protein interfaces
    • Sammond D.W., et al. Computational design of second-site suppressor mutations at protein-protein interfaces. Proteins 2010, 78:1055-1065.
    • (2010) Proteins , vol.78 , pp. 1055-1065
    • Sammond, D.W.1
  • 11
    • 34548383489 scopus 로고    scopus 로고
    • Design of multi-specificity in protein interfaces
    • Humphris E.L., Kortemme T. Design of multi-specificity in protein interfaces. PLoS Comput. Biol. 2007, 3:1591-1604.
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 1591-1604
    • Humphris, E.L.1    Kortemme, T.2
  • 12
    • 65249171530 scopus 로고    scopus 로고
    • Design of protein-interaction specificity gives selective bZIP-binding peptides
    • Grigoryan G., et al. Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 2009, 458:859-864.
    • (2009) Nature , vol.458 , pp. 859-864
    • Grigoryan, G.1
  • 13
    • 58549091879 scopus 로고    scopus 로고
    • Computational design of calmodulin mutants with up to 900-fold increase in binding specificity
    • Yosef E., et al. Computational design of calmodulin mutants with up to 900-fold increase in binding specificity. J. Mol. Biol. 2009, 385:1470-1480.
    • (2009) J. Mol. Biol. , vol.385 , pp. 1470-1480
    • Yosef, E.1
  • 14
    • 77956532389 scopus 로고    scopus 로고
    • Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs
    • Ashworth J., et al. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res. 2010, 38:5601-5608.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 5601-5608
    • Ashworth, J.1
  • 15
    • 73549117481 scopus 로고    scopus 로고
    • An artificial di-iron oxo-protein with phenol oxidase activity
    • Faiella M., et al. An artificial di-iron oxo-protein with phenol oxidase activity. Nat. Chem. Biol. 2009, 5:882-884.
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 882-884
    • Faiella, M.1
  • 16
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design of retro-aldol enzymes
    • Jiang L., et al. De novo computational design of retro-aldol enzymes. Science 2008, 319:1387-1391.
    • (2008) Science , vol.319 , pp. 1387-1391
    • Jiang, L.1
  • 17
    • 43449098518 scopus 로고    scopus 로고
    • Kemp elimination catalysts by computational enzyme design
    • Röthlisberger D., et al. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
    • (2008) Nature , vol.453 , pp. 190-195
    • Röthlisberger, D.1
  • 18
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel J.B., et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1
  • 19
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • Dunbrack R. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 2002, 12:431-440.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 431-440
    • Dunbrack, R.1
  • 20
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • Kuhlman B., et al. Design of a novel globular protein fold with atomic-level accuracy. Science 2003, 302:1364-1368.
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1
  • 21
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet J., et al. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992, 356:539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1
  • 22
    • 5744249209 scopus 로고
    • Equation of state calculation by fast computing machines
    • Metropolis N., et al. Equation of state calculation by fast computing machines. J. Chem. Phys. 1953, 21:1087-1092.
    • (1953) J. Chem. Phys. , vol.21 , pp. 1087-1092
    • Metropolis, N.1
  • 23
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick S., et al. Optimization by simulated annealing. Science 1983, 220:671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1
  • 24
    • 33745614865 scopus 로고    scopus 로고
    • Dramatic performance enhancements for the FASTER optimization algorithm
    • Allen B.D., Mayo S.L. Dramatic performance enhancements for the FASTER optimization algorithm. J. Comput. Chem. 2006, 27:1071-1075.
    • (2006) J. Comput. Chem. , vol.27 , pp. 1071-1075
    • Allen, B.D.1    Mayo, S.L.2
  • 25
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • Desjarlais J.R., Handel T.M. De novo design of the hydrophobic cores of proteins. Protein Sci. 1995, 4:2006-2018.
    • (1995) Protein Sci. , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 26
    • 0029869187 scopus 로고    scopus 로고
    • Mean-field minimization methods for biological macromolecules
    • Koehl P. Mean-field minimization methods for biological macromolecules. Curr. Opin. Struct. Biol. 1996, 6:222-226.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 222-226
    • Koehl, P.1
  • 27
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: overview and issues
    • Mackerell A.D. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 2004, 25:1584-1604.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
    • Mackerell, A.D.1
  • 28
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:10383-10388.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 29
    • 33744906496 scopus 로고    scopus 로고
    • A new generation of statistical potentials for proteins
    • Dehouck Y., et al. A new generation of statistical potentials for proteins. Biophys. J. 2006, 90:4010-4017.
    • (2006) Biophys. J. , vol.90 , pp. 4010-4017
    • Dehouck, Y.1
  • 30
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T., Karplus M. Effective energy function for proteins in solution. Proteins 1999, 35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 31
    • 34147169516 scopus 로고    scopus 로고
    • Potential energy functions for protein design
    • Boas F.E., Harbury P.B. Potential energy functions for protein design. Curr. Opin. Struct. Biol. 2007, 17:199-204.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 199-204
    • Boas, F.E.1    Harbury, P.B.2
  • 32
    • 51549107071 scopus 로고    scopus 로고
    • Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface
    • Reynolds K.A., et al. Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface. J. Mol. Biol. 2008, 382:1265-1275.
    • (2008) J. Mol. Biol. , vol.382 , pp. 1265-1275
    • Reynolds, K.A.1
  • 33
    • 44949229094 scopus 로고    scopus 로고
    • Design of protein-ligand binding based on the molecular-mechanics energy model
    • Boas F.E., Harbury P.B. Design of protein-ligand binding based on the molecular-mechanics energy model. J. Mol. Biol. 2008, 380:415-424.
    • (2008) J. Mol. Biol. , vol.380 , pp. 415-424
    • Boas, F.E.1    Harbury, P.B.2
  • 34
    • 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
  • 35
    • 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
  • 36
    • 69549120472 scopus 로고    scopus 로고
    • Conformational selection or induced fit: a flux description of reaction mechanism
    • Hammes G.G., et al. Conformational selection or induced fit: a flux description of reaction mechanism. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:13737-13741.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 13737-13741
    • Hammes, G.G.1
  • 37
    • 34547121250 scopus 로고    scopus 로고
    • Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL
    • Fu X., et al. Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. J. Mol. Biol. 2007, 371:1099-1117.
    • (2007) J. Mol. Biol. , vol.371 , pp. 1099-1117
    • Fu, X.1
  • 38
    • 78650566901 scopus 로고    scopus 로고
    • Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles
    • Allen B.D., et al. Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:19838-19843.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 19838-19843
    • Allen, B.D.1
  • 39
    • 32044456003 scopus 로고    scopus 로고
    • The backrub motion: how protein backbone shrugs when a sidechain dances
    • Davis I.W., et al. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 2006, 14:265-274.
    • (2006) Structure , vol.14 , pp. 265-274
    • Davis, I.W.1
  • 40
    • 45649084560 scopus 로고    scopus 로고
    • Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
    • Smith C.A., Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J. Mol. Biol. 2008, 380:742-756.
    • (2008) J. Mol. Biol. , vol.380 , pp. 742-756
    • Smith, C.A.1    Kortemme, T.2
  • 41
    • 46249112114 scopus 로고    scopus 로고
    • Algorithm for backrub motions in protein design
    • Georgiev I., et al. Algorithm for backrub motions in protein design. Bioinformatics 2008, 24:i196-i204.
    • (2008) Bioinformatics , vol.24
    • Georgiev, I.1
  • 42
    • 45649083705 scopus 로고    scopus 로고
    • A simple model of backbone flexibility improves modeling of side-chain conformational variability
    • Friedland G.D., et al. A simple model of backbone flexibility improves modeling of side-chain conformational variability. J. Mol. Biol. 2008, 380:757-774.
    • (2008) J. Mol. Biol. , vol.380 , pp. 757-774
    • Friedland, G.D.1
  • 43
    • 67049155677 scopus 로고    scopus 로고
    • A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
    • Friedland G.D., et al. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput. Biol. 2009, 5:1-16.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1-16
    • Friedland, G.D.1
  • 44
    • 67249107701 scopus 로고    scopus 로고
    • Alteration of enzyme specificity by computational loop remodeling and design
    • Murphy P.M., et al. Alteration of enzyme specificity by computational loop remodeling and design. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:9215-9220.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 9215-9220
    • Murphy, P.M.1
  • 45
    • 33750056673 scopus 로고    scopus 로고
    • ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
    • Meiler J., Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 2006, 65:538-548.
    • (2006) Proteins , vol.65 , pp. 538-548
    • Meiler, J.1    Baker, D.2
  • 46
    • 59849126340 scopus 로고    scopus 로고
    • Docking and scoring with alternative side-chain conformations
    • Hartmann C., et al. Docking and scoring with alternative side-chain conformations. Proteins 2009, 74:712-726.
    • (2009) Proteins , vol.74 , pp. 712-726
    • Hartmann, C.1
  • 47
    • 84871194822 scopus 로고    scopus 로고
    • Small molecule rotamers enable simultaneous optimization of small molecule and protein degrees of freedom in ROSETTALIGAND Docking
    • A. Beyer, M. Schroeder (Eds.)
    • Kaufmann K., et al. Small molecule rotamers enable simultaneous optimization of small molecule and protein degrees of freedom in ROSETTALIGAND Docking. German Conference on Bioinformatics 2008, 148-157. A. Beyer, M. Schroeder (Eds.).
    • (2008) German Conference on Bioinformatics , pp. 148-157
    • Kaufmann, K.1
  • 48
    • 48449094112 scopus 로고    scopus 로고
    • Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
    • Chaudhury S., Gray J.J. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J. Mol. Biol. 2008, 381:1068-1087.
    • (2008) J. Mol. Biol. , vol.381 , pp. 1068-1087
    • Chaudhury, S.1    Gray, J.J.2
  • 49
    • 79956080813 scopus 로고    scopus 로고
    • Computational design of an endo-1,4-β-xylanase ligand binding site. Protein Eng. Des. Sel. (in press)
    • Morin, A. et al. (2011) Computational design of an endo-1,4-β-xylanase ligand binding site. Protein Eng. Des. Sel. (in press).
    • (2011)
    • Morin, A.1
  • 50
    • 72749109072 scopus 로고    scopus 로고
    • Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics
    • Morra G., et al. Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics. Biophys. Chem. 2010, 146:76-84.
    • (2010) Biophys. Chem. , vol.146 , pp. 76-84
    • Morra, G.1
  • 51
    • 77952268732 scopus 로고    scopus 로고
    • Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping
    • Scarabelli G., et al. Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys. J. 2010, 98:1966-1975.
    • (2010) Biophys. J. , vol.98 , pp. 1966-1975
    • Scarabelli, G.1
  • 52
    • 77956566842 scopus 로고    scopus 로고
    • Dynamics-based discovery of allosteric inhibitors: selection of new ligands for the C-terminal domain of Hsp90
    • Morra G., et al. Dynamics-based discovery of allosteric inhibitors: selection of new ligands for the C-terminal domain of Hsp90. J. Chem. Theory Comput. 2010, 6:2978-2989.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2978-2989
    • Morra, G.1
  • 53
    • 75849162018 scopus 로고    scopus 로고
    • Incorporating receptor flexibility in the molecular design of protein interfaces
    • Li L., et al. Incorporating receptor flexibility in the molecular design of protein interfaces. Protein Eng. Des. Sel. 2009, 22:575-586.
    • (2009) Protein Eng. Des. Sel. , vol.22 , pp. 575-586
    • Li, L.1
  • 54
    • 33749030723 scopus 로고    scopus 로고
    • Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations
    • Spiegel K., et al. Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations. Proteins 2006, 65:317-330.
    • (2006) Proteins , vol.65 , pp. 317-330
    • Spiegel, K.1
  • 55
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science 1995, 268:1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 56
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • Bashford D., Case D.A. Generalized born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 2000, 51:129-152.
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 57
    • 70349463121 scopus 로고    scopus 로고
    • Computational design of Candida boidinii xylose reductase for altered cofactor specificity
    • Khoury G.A., et al. Computational design of Candida boidinii xylose reductase for altered cofactor specificity. Protein Sci. 2009, 18:2125-2138.
    • (2009) Protein Sci. , vol.18 , pp. 2125-2138
    • Khoury, G.A.1
  • 58
    • 35148855712 scopus 로고    scopus 로고
    • Computational design of antibody-affinity improvement beyond in vivo maturation
    • Lippow S.M., et al. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat. Biotechnol. 2007, 25:1171-1176.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1171-1176
    • Lippow, S.M.1
  • 59
    • 13944256616 scopus 로고    scopus 로고
    • A " solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
    • Jiang L., et al. A " solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 2005, 58:893-904.
    • (2005) Proteins , vol.58 , pp. 893-904
    • Jiang, L.1
  • 60
    • 77950437360 scopus 로고    scopus 로고
    • Origins of catalysis by computationally designed retroaldolase enzymes
    • Lassila J.K., et al. Origins of catalysis by computationally designed retroaldolase enzymes. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:4937-4942.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 4937-4942
    • Lassila, J.K.1
  • 61
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek J.J., Harbury P.B. Automated design of specificity in molecular recognition. Nat. Struct. Biol. 2003, 10:45-52.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 62
    • 24644472964 scopus 로고    scopus 로고
    • Specificity versus stability in computational protein design
    • Bolon D.N., et al. Specificity versus stability in computational protein design. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:12724-12729.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 12724-12729
    • Bolon, D.N.1
  • 63
    • 33745278855 scopus 로고    scopus 로고
    • Computational redesign of endonuclease DNA binding and cleavage specificity
    • Ashworth J., et al. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006, 441:656-659.
    • (2006) Nature , vol.441 , pp. 656-659
    • Ashworth, J.1
  • 64
    • 57049180165 scopus 로고    scopus 로고
    • Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design
    • Humphris E.L., Kortemme T. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure 2008, 16:1777-1788.
    • (2008) Structure , vol.16 , pp. 1777-1788
    • Humphris, E.L.1    Kortemme, T.2
  • 65
    • 73249124179 scopus 로고    scopus 로고
    • Computational design of ligand binding is not a solved problem
    • Schreier B., et al. Computational design of ligand binding is not a solved problem. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:18491-18496.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 18491-18496
    • Schreier, B.1
  • 66
    • 33751525692 scopus 로고    scopus 로고
    • New algorithms and an in silico benchmark for computational enzyme design
    • Zanghellini A., et al. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 2006, 15:2785-2794.
    • (2006) Protein Sci. , vol.15 , pp. 2785-2794
    • Zanghellini, A.1
  • 67
    • 78650543850 scopus 로고    scopus 로고
    • Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries
    • Chica R.A., et al. Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:20257-20262.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 20257-20262
    • Chica, R.A.1
  • 68
    • 77954990456 scopus 로고    scopus 로고
    • Design and directed evolution of a dideoxy purine nucleoside phosphorylase
    • Nannemann D.P., et al. Design and directed evolution of a dideoxy purine nucleoside phosphorylase. Protein Eng. Des. Sel. 2010, 23:607-616.
    • (2010) Protein Eng. Des. Sel. , vol.23 , pp. 607-616
    • Nannemann, D.P.1
  • 69
    • 34548522063 scopus 로고    scopus 로고
    • Alternative non-antibody scaffolds for molecular recognition
    • Skerra A. Alternative non-antibody scaffolds for molecular recognition. Curr. Opin. Biotechnol. 2007, 18:295-304.
    • (2007) Curr. Opin. Biotechnol. , vol.18 , pp. 295-304
    • Skerra, A.1
  • 70
    • 62849116221 scopus 로고    scopus 로고
    • Engineered affinity proteins-generation and applications
    • Grönwall C., Ståhl S. Engineered affinity proteins-generation and applications. J. Biotechnol. 2009, 140:254-269.
    • (2009) J. Biotechnol. , vol.140 , pp. 254-269
    • Grönwall, C.1    Ståhl, S.2
  • 71
    • 12844276589 scopus 로고    scopus 로고
    • Lipocalins in drug discovery: from natural ligand-binding proteins to " anticalins"
    • Schlehuber S., Skerra A. Lipocalins in drug discovery: from natural ligand-binding proteins to " anticalins" Drug Discov. Today 2005, 10:23-33.
    • (2005) Drug Discov. Today , vol.10 , pp. 23-33
    • Schlehuber, S.1    Skerra, A.2
  • 72
    • 77951586447 scopus 로고    scopus 로고
    • Strategies and challenges for the next generation of therapeutic antibodies
    • Beck A., et al. Strategies and challenges for the next generation of therapeutic antibodies. Nat. Rev. Immunol. 2010, 10:345-352.
    • (2010) Nat. Rev. Immunol. , vol.10 , pp. 345-352
    • Beck, A.1
  • 74
    • 33846439351 scopus 로고    scopus 로고
    • Cocaine esterase: interactions with cocaine and immune responses in mice
    • Ko M.C., et al. Cocaine esterase: interactions with cocaine and immune responses in mice. J. Pharmacol. Exp. Ther. 2007, 320:926-933.
    • (2007) J. Pharmacol. Exp. Ther. , vol.320 , pp. 926-933
    • Ko, M.C.1
  • 75
    • 33751097261 scopus 로고    scopus 로고
    • Rapid and robust protection against cocaine-induced lethality in rats by the bacterial cocaine esterase
    • Cooper Z.D., et al. Rapid and robust protection against cocaine-induced lethality in rats by the bacterial cocaine esterase. Mol. Pharmacol. 2006, 70:1885-1891.
    • (2006) Mol. Pharmacol. , vol.70 , pp. 1885-1891
    • Cooper, Z.D.1
  • 76
    • 59449089478 scopus 로고    scopus 로고
    • Thermostable variants of cocaine esterase for long-time protection against cocaine toxicity
    • Gao D., et al. Thermostable variants of cocaine esterase for long-time protection against cocaine toxicity. Mol. Pharmacol. 2009, 75:318-323.
    • (2009) Mol. Pharmacol. , vol.75 , pp. 318-323
    • Gao, D.1
  • 77
    • 77955941601 scopus 로고    scopus 로고
    • Structural analysis of thermostabilizing mutations of cocaine esterase
    • Narasimhan D., et al. Structural analysis of thermostabilizing mutations of cocaine esterase. Protein Eng. Des. Sel. 2010, 23:537-547.
    • (2010) Protein Eng. Des. Sel. , vol.23 , pp. 537-547
    • Narasimhan, D.1
  • 78
    • 77950212804 scopus 로고    scopus 로고
    • A thermally stable form of bacterial cocaine esterase: a potential therapeutic agent for treatment of cocaine abuse
    • Brim R.L., et al. A thermally stable form of bacterial cocaine esterase: a potential therapeutic agent for treatment of cocaine abuse. Mol. Pharmacol. 2010, 77:593-600.
    • (2010) Mol. Pharmacol. , vol.77 , pp. 593-600
    • Brim, R.L.1
  • 79
    • 76749083724 scopus 로고    scopus 로고
    • PEGylation of bacterial cocaine esterase for protection against protease digestion and immunogenicity
    • Park J.B., et al. PEGylation of bacterial cocaine esterase for protection against protease digestion and immunogenicity. J. Control. Release 2010, 142:174-179.
    • (2010) J. Control. Release , vol.142 , pp. 174-179
    • Park, J.B.1
  • 80
    • 56749170877 scopus 로고    scopus 로고
    • Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination
    • Alexandrova A.N., et al. Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J. Am. Chem. Soc. 2008, 130:15907-15915.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 15907-15915
    • Alexandrova, A.N.1
  • 81
    • 77649271939 scopus 로고    scopus 로고
    • Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series
    • Khersonsky O., et al. Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. J. Mol. Biol. 2010, 396:1025-1042.
    • (2010) J. Mol. Biol. , vol.396 , pp. 1025-1042
    • Khersonsky, O.1
  • 82
    • 70349632843 scopus 로고    scopus 로고
    • The influence of protein dynamics on the success of computational enzyme design
    • Ruscio J.Z., et al. The influence of protein dynamics on the success of computational enzyme design. J. Am. Chem. Soc. 2009, 131:14111-14115.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 14111-14115
    • Ruscio, J.Z.1
  • 83
    • 77950469105 scopus 로고    scopus 로고
    • De novo backbone scaffolds for protein design
    • MacDonald J.T., et al. De novo backbone scaffolds for protein design. Proteins 2010, 78:1311-1325.
    • (2010) Proteins , vol.78 , pp. 1311-1325
    • MacDonald, J.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.