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Volumn 6, Issue SUPPL. 4, 2009, Pages

Challenges in the computational design of proteins

Author keywords

Computational; Design; Proteins

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; ATOMS; BIOLOGY; ORGANIC ACIDS; PROTEINS;

EID: 67650397253     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2008.0508.focus     Document Type: Review
Times cited : (45)

References (128)
  • 1
    • 0033117763 scopus 로고    scopus 로고
    • Matching theory and experiment in protein folding
    • doi:10.1016/S0959-440X(99)80027-X
    • Alm, E. & Baker, D. 1999 Matching theory and experiment in protein folding. Curr. Opin. Struct. Biol. 9, 189-196. (doi:10.1016/S0959-440X(99)80027- X)
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 189-196
    • Alm, E.1    Baker, D.2
  • 2
    • 33644965220 scopus 로고    scopus 로고
    • Design of a hyperstable protein by rational consideration of unfolded state interactions
    • doi:10.1021/ja057874b
    • Anil, B., Craig-Schapiro, R. & Raleigh, D. P. 2006 Design of a hyperstable protein by rational consideration of unfolded state interactions. J. Am. Chem. Soc. 128, 3144-3145. (doi:10.1021/ja057874b)
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 3144-3145
    • Anil, B.1    Craig-Schapiro, R.2    Raleigh, D.P.3
  • 4
    • 33745278855 scopus 로고    scopus 로고
    • Computational redesign of endonuclease DNA binding and cleavage specificity
    • DOI 10.1038/nature04818, PII N04818
    • Ashworth, J., Havranek, J., Duarte, C., Sussman, D., Monnat, R., Stoddard, B. & Baker, D. 2006 Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441, 656-659. (doi:10.1038/ nature04818) (Pubitemid 43927299)
    • (2006) Nature , vol.441 , Issue.7093 , pp. 656-659
    • Ashworth, J.1    Havranek, J.J.2    Duarte, C.M.3    Sussman, D.4    Monnat Jr., R.J.5    Stoddard, B.L.6    Baker, D.7
  • 5
    • 0027716138 scopus 로고
    • The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme
    • Baldwin, E. P., Hajiseyedjavadi, O., Baase, W. A. & Matthews, B. W. 1993 The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science 262, 1715-1718. (doi:10.1126/science. 8259514) (Pubitemid 24030091)
    • (1993) Science , vol.262 , Issue.5140 , pp. 1715-1718
    • Baldwin, E.P.1    Hajiseyedjavadi, O.2    Baase, W.A.3    Matthews, B.W.4
  • 6
    • 0034612312 scopus 로고    scopus 로고
    • Rational design of nascent metalloenzymes
    • doi:10.1073/pnas.97.12.6292
    • Benson, D. E., Wisz, S. E. & Hellinga, H. W. 1999 Rational design of nascent metalloenzymes. Proc. Natl Acad. Sci. USA 97, 6292-6297. (doi:10.1073/pnas.97.12.6292)
    • (1999) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6292-6297
    • Benson, D.E.1    Wisz, S.E.2    Hellinga, H.W.3
  • 7
    • 42049088165 scopus 로고    scopus 로고
    • Entropic stabilization of proteins and its proteomic consequences
    • doi:10.1371/journal.pcbi.0010047
    • Berezovsky, I. N., Chen, W. W., Choi, P. J. & Shakhnovich, E. I. 2005 Entropic stabilization of proteins and its proteomic consequences. PLoS Comput. Biol. 1, e47. (doi:10.1371/journal.pcbi.0010047)
    • (2005) PLoS Comput. Biol. , vol.1
    • Berezovsky, I.N.1    Chen, W.W.2    Choi, P.J.3    Shakhnovich, E.I.4
  • 8
    • 34147169516 scopus 로고    scopus 로고
    • Potential energy functions for protein design
    • doi:10.1016/j.sbi.2007.03.006
    • Boas, F. E. & Harbury, P. B. 2007 Potential energy functions for protein design. Curr. Opin. Struct. Biol. 17, 199-204. (doi:10.1016/j.sbi.2007. 03.006)
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 199-204
    • Boas, F.E.1    Harbury, P.B.2
  • 9
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • 279 doi:10.1073/pnas.251555398
    • Bolon, D. & Mayo, S. 2001a Enzyme-like proteins by computational design. Proc. Natl. Acad. Sci. USA 98, 14 274-14 279. (doi:10.1073/pnas. 251555398)
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , Issue.14 , pp. 274-314
    • Bolon, D.1    Mayo, S.2
  • 10
    • 0035964177 scopus 로고    scopus 로고
    • Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity
    • DOI 10.1021/bi010427y
    • Bolon, D. & Mayo, S. 2001b Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity. Biochemistry 40, 10 047-10 053. (doi:10.1021/ bi010427y) (Pubitemid 32800112)
    • (2001) Biochemistry , vol.40 , Issue.34 , pp. 10047-10053
    • Bolon, D.N.1    Mayo, S.L.2
  • 11
    • 24644472964 scopus 로고    scopus 로고
    • Specificity versus stability in computational protein design
    • 729 doi:10.1073/pnas.0506124102
    • Bolon, D., Grant, R. A., Baker, T. & Sauer, R. T. 2005 Specificity versus stability in computational protein design. Proc. Natl Acad. Sci. USA 102, 12 724-12 729. (doi:10.1073/pnas.0506124102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.12 , pp. 724-812
    • Bolon, D.1    Grant, R.A.2    Baker, T.3    Sauer, R.T.4
  • 12
    • 10044248344 scopus 로고    scopus 로고
    • Catalytic promiscuity in biocatalysis: Using old enzymes to form new bonds and follow new pathways
    • doi:10.1002/anie.200460416
    • Bornscheuer, U. T. & Kazlauskas, R. 2004 Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew. Chem. Int. Ed. Engl. 43, 6032-6040. (doi:10.1002/anie.200460416)
    • (2004) Angew. Chem. Int. Ed. Engl. , vol.43 , pp. 6032-6040
    • Bornscheuer, U.T.1    Kazlauskas, R.2
  • 13
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J., Lathy, R. & Heisenberg, D. 1991 A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170. (doi:10. 1126/science.1853201) (Pubitemid 21917131)
    • (1991) Science , vol.253 , Issue.5016 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 14
    • 0033970022 scopus 로고    scopus 로고
    • Expectations from structural genomics
    • Brenner, S. E. & Levitt, M. 2000 Expectations from structural genomics. Protein Sci. 9, 197-200.
    • (2000) Protein Sci. , vol.9 , pp. 197-200
    • Brenner, S.E.1    Levitt, M.2
  • 15
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    • doi:10.1002/jcc. 540040211
    • Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. 1983 CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187-217. (doi:10.1002/jcc. 540040211)
    • (1983) J. Comp. Chem. , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Olafson, B.D.3    States, D.J.4    Swaminathan, S.5    Karplus, M.6
  • 16
    • 0036136382 scopus 로고    scopus 로고
    • Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation
    • DOI 10.1128/JB.184.2.344-349.2002
    • Canada, K. A., Iwashita, S., Shim, S. & Wood, T. K. 2002 Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation. J. Bacteriol. 184, 344-349. (doi:10.1128/ JB.184.2.344-349.2002) (Pubitemid 34027373)
    • (2002) Journal of Bacteriology , vol.184 , Issue.2 , pp. 344-349
    • Canada, K.A.1    Iwashita, S.2    Shim, H.3    Wood, T.K.4
  • 17
    • 22544451519 scopus 로고    scopus 로고
    • Computational prediction of native protein ligand-binding and enzyme active site sequences
    • 158 doi:10.1073/pnas.0504023102
    • Chakrabarti, R., Klibanov, A. & Friesner, R. 2005 Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc. Natl Acad. Sci. USA 102, 10 153-10 158. (doi:10.1073/pnas.0504023102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.10 , pp. 153-210
    • Chakrabarti, R.1    Klibanov, A.2    Friesner, R.3
  • 18
    • 36049005713 scopus 로고    scopus 로고
    • Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii
    • DOI 10.1529/biophysj.107.108589
    • Chang, C. H., King, P. W., Ghirardi, M. L. & Kim, K. 2007 Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii. Biophys. J. 93, 3034-3045. (doi:10.1529/biophysj.107. 108589) (Pubitemid 350097096)
    • (2007) Biophysical Journal , vol.93 , Issue.9 , pp. 3034-3045
    • Chang, C.H.1    King, P.W.2    Ghirardi, M.L.3    Kim, K.4
  • 19
    • 0036810246 scopus 로고    scopus 로고
    • Design, activity, and structure of a highly specific artificial endonuclease
    • DOI 10.1016/S1097-2765(02)00690-1
    • Chevalier, B. S., Kortemme, T., Chadsey, M. S., Baker, D., Monnat, R. & Stoddard, B. L. 2002 Design, activity and structure of a highly specific artificial endonuclease. Mol. Cell 10, 895-905. (doi:10.1016/S1097-2765(02) 00690-1) (Pubitemid 35335643)
    • (2002) Molecular Cell , vol.10 , Issue.4 , pp. 895-905
    • Chevalier, B.S.1    Kortemme, T.2    Chadsey, M.S.3    Baker, D.4    Monnat Jr., R.J.5    Stoddard, B.L.6
  • 20
    • 13444302392 scopus 로고    scopus 로고
    • Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor
    • doi:10.1021/ja044129a
    • Cochran, F., Wu, S., Wang, W., Nanda, V., Saven, J. G., Therien, M. & DeGrado, W. 2005 Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J. Am. Chem. Soc. 127, 1346-1347. (doi:10.1021/ja044129a)
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 1346-1347
    • Cochran, F.1    Wu, S.2    Wang, W.3    Nanda, V.4    Saven, J.G.5    Therien, M.6    Degrado, W.7
  • 21
    • 0029620316 scopus 로고
    • Modeling unfolded states of peptides and proteins
    • DOI 10.1021/bi00050a003
    • Creamer, T. P., Srinivasan, R. & Rose, G. D. 1995 Modeling unfolded states of peptides and proteins. Biochemistry 34, 16 245-16 250. (doi:10.1021/bi00050a003) (Pubitemid 26006466)
    • (1995) Biochemistry , vol.34 , Issue.50 , pp. 16245-16250
    • Creamer, T.P.1    Srinivasan, R.2    Rose, G.D.3
  • 22
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • DOI 10.1126/science.278.5335.82
    • Dahiyat, B. & Mayo, S. 1997 De novo protein design: fully automated sequence selection. Science 278, 82-87. (doi:10. 1126/science.278.5335.82) (Pubitemid 27446279)
    • (1997) Science , vol.278 , Issue.5335 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 23
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
    • doi:10. 1016/S0022-2836(03)
    • Dantas, G., Kuhlman, B., Callender, D., Wong, M. & Baker, D. 2003 A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J. Mol. Biol. 332, 449-460. (doi:10. 1016/S0022-2836(03))
    • (2003) J. Mol. Biol. , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman, B.2    Callender, D.3    Wong, M.4    Baker, D.5
  • 24
    • 0028858499 scopus 로고
    • De novo design of the hydrophobic cores of proteins
    • doi:10.1002/pro.5560041006
    • Desjarlais, J. R. & Handel, T. M. 1995 De novo design of the hydrophobic cores of proteins. Protein Sci. 4, 2006-2018. (doi:10.1002/pro. 5560041006)
    • (1995) Protein Sci , vol.4 , pp. 2006-2018
    • Desjarlais, J.R.1    Handel, T.M.2
  • 25
    • 0033516509 scopus 로고    scopus 로고
    • Side-chain and backbone flexibility in protein core design
    • doi:10.1006/jmbi.1999.2866
    • Desjarlais, J. R. & Handel, T. M. 1999 Side-chain and backbone flexibility in protein core design. J. Mol. Biol. 290, 305-318. (doi:10.1006/jmbi.1999.2866)
    • (1999) J. Mol. Biol. , vol.290 , pp. 305-318
    • Desjarlais, J.R.1    Handel, T.M.2
  • 26
    • 0026589733 scopus 로고
    • The dead end elimination theorem and its use in protein side chain positioning
    • doi:10.1038/ 356539a0
    • Desmet, J., De Maeyer, M., Hazes, B. & Lasters, I. 1992 The dead end elimination theorem and its use in protein side chain positioning. Nature 356, 539-542. (doi:10.1038/ 356539a0)
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 27
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • doi:10.1002/1097-0134 (20001001)41:1!98::AID-PROT120O3.0.CO;2-S
    • Devos, D. & Valencia, A. 2000 Practical limits of function prediction. Proteins 41, 98-107. (doi:10.1002/1097-0134 (20001001)41:1!98::AID- PROT120O3.0.CO;2-S)
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 28
    • 0028871798 scopus 로고
    • Side chain conformational entropy in protein folding
    • doi:10.1002/pro.5560041101
    • Doig, A. J. & Sternberg, M. J. E. 1995 Side chain conformational entropy in protein folding. Protein Sci. 4, 2247-2251. (doi:10.1002/pro. 5560041101)
    • (1995) Protein Sci , vol.4 , pp. 2247-2251
    • Doig, A.J.1    Sternberg, M.J.E.2
  • 29
    • 0034727794 scopus 로고    scopus 로고
    • Improving the refolding yield of interleukin-4 through the optimization of local interactions
    • DOI 10.1016/S0168-1656(00)00327-8, PII S0168165600003278
    • Domingues, H., Peter, J., Schneider, K. H., Apeler, H., Sebald, W., Oschkinat, H. & Serrano, L. 2000 Improving the refolding yield of interleukin-4 through the optimization of local interactions. J. Biotechnol. 84, 217-230. (doi:10.1016/S0168-1656(00)00327-8) (Pubitemid 32332941)
    • (2000) Journal of Biotechnology , vol.84 , Issue.3 , pp. 217-230
    • Domingues, H.1    Peters, J.2    Schneider, K.-H.3    Apeler, H.4    Sebald, W.5    Oschkinat, H.6    Serrano, L.7
  • 30
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • doi:10.1016/S0959-440X(02)00344-5
    • Dunbrack, R. L. 2002 Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12, 431-440. (doi:10.1016/S0959-440X(02)00344-5)
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 431-440
    • Dunbrack, R.L.1
  • 31
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins: Application to side-chain prediction
    • doi:10.1006/jmbi. 1993.1170
    • Dunbrack, R. L. & Karplus, M. 1993 Backbone-dependent rotamer library for proteins: application to side-chain prediction. J. Mol. Biol. 230, 543-547. (doi:10.1006/jmbi. 1993.1170)
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-547
    • Dunbrack, R.L.1    Karplus, M.2
  • 32
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • doi:10.1016/j.sbi.2004.03.009
    • Feig, M. & Brooks III, C. L. 2004 Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14, 217-224. (doi:10.1016/j.sbi.2004.03.009)
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 33
    • 38349008761 scopus 로고    scopus 로고
    • Towards full sequence de novo protein design with flexible templates for human beta-defensin-2
    • doi:10.1529/biophysj.107.110627
    • Fung, H. K., Floudas, C. A., Taylor, M. S., Zhang, L. & Morikis, D. 2008 Towards full sequence de novo protein design with flexible templates for human beta-defensin-2. Biophys. J. 94, 584-599. (doi:10.1529/biophysj.107. 110627)
    • (2008) Biophys. J. , vol.94 , pp. 584-599
    • Fung, H.K.1    Floudas, C.A.2    Taylor, M.S.3    Zhang, L.4    Morikis, D.5
  • 34
    • 57049135960 scopus 로고
    • Digital computer studies of cell multiplication by Monte Carlo methods
    • Gardiner, V., Hoffman, J. V. & Metropolis, N. 1956 Digital computer studies of cell multiplication by Monte Carlo methods. J. Natl. Cancer Inst. 17, 175-188.
    • (1956) J. Natl. Cancer Inst. , vol.17 , pp. 175-188
    • Gardiner, V.1    Hoffman, J.V.2    Metropolis, N.3
  • 35
    • 0028212927 scopus 로고
    • Efficient rotamer elimination applied to protein side-chains and related spin glasses
    • doi:10.1016/S0006-3495(94)80923-3
    • Goldstein, R. F. 1994 Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys. J. 66, 1335-1340. (doi:10.1016/S0006-3495(94)80923-3)
    • (1994) Biophys. J. , vol.66 , pp. 1335-1340
    • Goldstein, R.F.1
  • 36
    • 0033200183 scopus 로고    scopus 로고
    • Branch and terminate: A combinatorial optimization algorithm for protein design
    • doi:10.1016/S0969-2126 (99)80176-2
    • Gordon, D. B. & Mayo, S. L. 1999 Branch and terminate: a combinatorial optimization algorithm for protein design. Struct. Fold. Des. 7, 1089-1098. (doi:10.1016/S0969-2126 (99)80176-2)
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1089-1098
    • Gordon, D.B.1    Mayo, S.L.2
  • 37
    • 0033178329 scopus 로고    scopus 로고
    • Energy functions for protein design
    • doi:10.1016/S0959-440X(99)80072-4
    • Gordon, D. B., Marshall, S. A. & Mayo, S. L. 1999 Energy functions for protein design. Curr. Opin. Struct. Biol. 9, 509-513. (doi:10.1016/S0959- 440X(99)80072-4)
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 509-513
    • Gordon, D.B.1    Marshall, S.A.2    Mayo, S.L.3
  • 38
    • 33750058234 scopus 로고    scopus 로고
    • Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide
    • DOI 10.1021/bi060857u
    • Green, D. E., Dennis, A. T., Fam, P. S., Tidor, B. & Jasanoff, A. 2006 Rational design of a new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry 45, 12 547-12 559. (doi:10.1021/ bi060857u) (Pubitemid 44583697)
    • (2006) Biochemistry , vol.45 , Issue.41 , pp. 12547-12559
    • Green, D.F.1    Dennis, A.T.2    Fam, P.S.3    Tidor, B.4    Jasanoff, A.5
  • 39
    • 33644831449 scopus 로고    scopus 로고
    • Modular enzyme design: Regulation by mutually exclusive protein folding
    • doi:10.1016/j.jmb.2006.01.073
    • Ha, J.-H., Butler, J. S., Mitrea, D. M. & Stewart, L. N. 2006 Modular enzyme design: regulation by mutually exclusive protein folding. J. Mol. Biol. 357, 1058-1062. (doi:10.1016/j.jmb.2006.01.073)
    • (2006) J. Mol. Biol. , vol.357 , pp. 1058-1062
    • Ha, J.-H.1    Butler, J.S.2    Mitrea, D.M.3    Stewart, L.N.4
  • 40
    • 0033117762 scopus 로고    scopus 로고
    • Designing potential energy functions for protein folding
    • doi:10.1016/S0959-440X(99)80026-8
    • Hao, M. H. & Scheraga, H. A. 1999 Designing potential energy functions for protein folding. Curr. Opin. Struct. Biol. 9, 184-188. (doi:10.1016/S0959-440X(99)80026-8)
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 184-188
    • Hao, M.H.1    Scheraga, H.A.2
  • 41
    • 0027756896 scopus 로고
    • A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
    • Harbury, P. B., Zhang, T., Kim, P. S. & Alber, T. 1993 A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262, 1401-1407. (doi:10.1126/science.8248779) (Pubitemid 24035058)
    • (1993) Science , vol.262 , Issue.5138 , pp. 1401-1406
    • Harbury, P.B.1    Zhang, T.2    Kim, P.S.3    Alber, T.4
  • 42
    • 0032553587 scopus 로고    scopus 로고
    • High-resolution protein design with backbone freedom
    • Harbury, P. B., Plecs, J. J., Tidor, B., Alber, T. & Kim, P. S. 1998 High-resolution protein design with backbone freedom. Science 282, 1462. (doi:10.1126/science.282. 5393.1462) (Pubitemid 28538602)
    • (1998) Science , vol.282 , Issue.5393 , pp. 1462-1467
    • Harbury, P.B.1    Plecs, J.J.2    Tidor, B.3    Alber, T.4    Kim, P.S.5
  • 43
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • doi:10.1038/nsb877
    • Havranek, J. J. & Harbury, B. P. 2002 Automated design of specificity in molecular recognition. Nat. Struct. Biol. 10, 45-52. (doi:10.1038/nsb877)
    • (2002) Nat. Struct. Biol. , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, B.P.2
  • 44
    • 0037059061 scopus 로고    scopus 로고
    • Combining computational and experimental screening for rapid optimization of protein properties
    • 931 doi:10.1073/pnas.212627499
    • Hayes, R. J., Bentzien, J., Ary, M. L., Hwang, M. Y., Jacinto, J. M., Vielmetter, J., Kundu, A. & Dahiyat, B. I. 2002 Combining computational and experimental screening for rapid optimization of protein properties. Proc. Natl Acad. Sci. USA 99, 15 926-15 931. (doi:10.1073/pnas.212627499)
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , Issue.15 , pp. 926-915
    • Hayes, R.J.1    Bentzien, J.2    Ary, M.L.3    Hwang, M.Y.4    Jacinto, J.M.5    Vielmetter, J.6    Kundu, A.7    Dahiyat, B.I.8
  • 45
    • 0025040232 scopus 로고
    • De novo design, expression, and characterization of Felix: A four-helix bundle protein of native-like sequence
    • doi:10.1126/science. 2392678
    • Hecht, M. H., Richardson, J. S., Richardson, D. C. & Ogden, R. C. 1990 De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 249, 884-891. (doi:10.1126/science. 2392678)
    • (1990) Science , vol.249 , pp. 884-891
    • Hecht, M.H.1    Richardson, J.S.2    Richardson, D.C.3    Ogden, R.C.4
  • 46
    • 0028237287 scopus 로고
    • Optimal sequence selection in protein of known structure by simulated evolution
    • doi:10.1073/pnas.91.13.5803
    • Hellinga, H. W. & Richards, F. M. 1994 Optimal sequence selection in protein of known structure by simulated evolution. Proc. Natl Acad. Sci. USA 91, 5803-5807. (doi:10.1073/pnas.91.13.5803)
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 5803-5807
    • Hellinga, H.W.1    Richards, F.M.2
  • 47
    • 84990424072 scopus 로고
    • A consistent empirical potential for water-protein interactions
    • doi:10. 1002/bip.360230807
    • Hermans, J., Berendsen, H. J. C., Vangunsteren, W. F. & Postma, J. P. M. 1984 A consistent empirical potential for water-protein interactions. Biopolymers 23, 1513. (doi:10. 1002/bip.360230807)
    • (1984) Biopolymers , vol.23 , pp. 1513
    • Hermans, J.1    Berendsen, H.J.C.2    Vangunsteren, W.F.3    Postma, J.P.M.4
  • 48
    • 0032544060 scopus 로고    scopus 로고
    • The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble
    • doi:10.1073/pnas.95. 17.9903
    • Hilser, V. J., Dowddy, D. D., Oas, T. G. & Freire, E. 1998 The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. Proc. Natl Acad. Sci. USA 95, 9903-9908. (doi:10.1073/pnas.95. 17.9903)
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 9903-9908
    • Hilser, V.J.1    Dowddy, D.D.2    Oas, T.G.3    Freire, E.4
  • 49
    • 31944436020 scopus 로고    scopus 로고
    • Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences
    • DOI 10.1002/prot.20786
    • Hu, X. & Kuhlman, B. 2006 Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins 62, 739-748. (doi:10.1002/prot.20786) (Pubitemid 43191260)
    • (2006) Proteins: Structure, Function and Genetics , vol.62 , Issue.3 , pp. 739-748
    • Hu, X.1    Kuhlman, B.2
  • 50
    • 57049181918 scopus 로고    scopus 로고
    • Computer-based redesign of a b sandwich protein suggests that extensive negative design is not required for de novo β sheet design
    • doi:10.1016/j.str. 2008.09.013
    • Hu, X., Wang, H., Ke, H. & Kuhlman, B. 2008 Computer-based redesign of a b sandwich protein suggests that extensive negative design is not required for de novo β sheet design. Structure 16, 1799-1805. (doi:10.1016/j.str. 2008.09.013)
    • (2008) Structure , vol.16 , pp. 1799-1805
    • Hu, X.1    Wang, H.2    Ke, H.3    Kuhlman, B.4
  • 51
    • 34548383489 scopus 로고    scopus 로고
    • Design of multi-specificity in protein interfaces
    • doi:10.1371/journal.pcbi.0030164
    • Humphris, E. L. & Kortemme, T. 2007 Design of multi-specificity in protein interfaces. PLoS Comput. Biol. 3, e164. (doi:10.1371/journal.pcbi. 0030164)
    • (2007) PLoS Comput. Biol. , vol.3
    • Humphris, E.L.1    Kortemme, T.2
  • 52
    • 0026532266 scopus 로고
    • Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme
    • doi:10.1016/0022-2836 (92)90475-Y
    • Hurley, J. H., Baase, W. A. & Matthews, B. W. 1992 Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J. Mol. Biol. 224, 1143-1159. (doi:10.1016/0022-2836 (92)90475-Y)
    • (1992) J. Mol. Biol. , vol.224 , pp. 1143-1159
    • Hurley, J.H.1    Baase, W.A.2    Matthews, B.W.3
  • 53
    • 11244318120 scopus 로고    scopus 로고
    • Computational protein design is a challenge for implicit solvation models
    • DOI 10.1529/biophysj.104.042044
    • Jaramillo, A. & Wodak, S. J. 2005 Computational protein design is a challenge for implicit solvation models. Biophys. J. 88, 156-171. (doi:10.1529/biophysj.104.042044) (Pubitemid 40070666)
    • (2005) Biophysical Journal , vol.88 , Issue.1 , pp. 156-171
    • Jaramillo, A.1    Wodak, S.J.2
  • 55
    • 0037108748 scopus 로고    scopus 로고
    • Native protein sequences are near optimal for their structures in the protein core but not on the surface
    • 559 doi:10. 1073/pnas.212068599
    • Jaramillo, A., Wernisch, L., Hery, S. & Wodak, S. J. 2002 Native protein sequences are near optimal for their structures in the protein core but not on the surface. Proc. Natl Acad. Sci. USA 99, 13 554-13 559. (doi:10. 1073/pnas.212068599)
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , Issue.13 , pp. 554-613
    • Jaramillo, A.1    Wernisch, L.2    Hery, S.3    Wodak, S.J.4
  • 56
    • 0033048066 scopus 로고    scopus 로고
    • Moonlighting proteins
    • doi:10.1016/S0968-0004(98)01335-8
    • Jeffery, C. J. 1999 Moonlighting proteins. Biochem. Sci. 24, 8-11. (doi:10.1016/S0968-0004(98)01335-8)
    • (1999) Biochem. Sci. , vol.24 , pp. 8-11
    • Jeffery, C.J.1
  • 57
    • 13944256616 scopus 로고    scopus 로고
    • A 'solvated rotamer' approach to modeling watermediated hydrogen bonds at protein-protein interfaces
    • doi:10.1002/prot.20347
    • Jiang, L., Kuhlman, B., Kortemme, T. & Baker, D. 2005 A 'solvated rotamer' approach to modeling watermediated hydrogen bonds at protein-protein interfaces. Proteins 58, 893-904. (doi:10.1002/prot.20347)
    • (2005) Proteins , vol.58 , pp. 893-904
    • Jiang, L.1    Kuhlman, B.2    Kortemme, T.3    Baker, D.4
  • 59
    • 0038242197 scopus 로고    scopus 로고
    • De novo design of foldable proteins with smooth folding funnel: Automated negative design and experimental verification
    • DOI 10.1016/S0969-2126(03)00075-3
    • Jin, W., Kambara, O., Sasakawa, H., Tamura, A. & Takada, S. 2003 De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification. Structure 11, 581-590. (doi:10.1016/ S0969-2126(03)00075-3) (Pubitemid 36579135)
    • (2003) Structure , vol.11 , Issue.5 , pp. 581-590
    • Jin, W.1    Kambara, O.2    Sasakawa, H.3    Tamura, A.4    Takada, S.5
  • 60
    • 33745927413 scopus 로고    scopus 로고
    • Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface
    • doi:10.1016/j.jmb.2006.05.022
    • Joachimiak, L., Kortemme, T., Stoddard, B. & Baker, D. 2006 Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J. Mol. Biol. 361, 195-208. (doi:10.1016/j.jmb.2006.05.022)
    • (2006) J. Mol. Biol. , vol.361 , pp. 195-208
    • Joachimiak, L.1    Kortemme, T.2    Stoddard, B.3    Baker, D.4
  • 62
    • 4143131151 scopus 로고    scopus 로고
    • De novo design of catalytic proteins
    • 570. doi:10.1073/pnas.0404387101
    • Kaplan, J. & DeGrado, W. F. 2004 De novo design of catalytic proteins. Proc. Natl Acad. Sci. USA 101, 11 566-11 570. (doi:10.1073/pnas. 0404387101)
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , Issue.11 , pp. 566-611
    • Kaplan, J.1    Degrado, W.F.2
  • 63
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • doi:10.1016/S0006-3495(87)83303-9
    • Karplus, M., Ichiye, T. & Pettitt, B. M. 1987 Configurational entropy of native proteins. Biophys. J. 52, 1083-1085. (doi:10.1016/S0006-3495(87) 83303-9)
    • (1987) Biophys. J. , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 64
    • 16244379809 scopus 로고    scopus 로고
    • Enhancing catalytic promiscuity for biocatalysis
    • doi:10. 1016/j.cbpa.2005.02.008
    • Kazlauskas, R. J. 2005 Enhancing catalytic promiscuity for biocatalysis. Curr. Opin. Chem. Biol. 9, 195-201. (doi:10. 1016/j.cbpa.2005.02.008)
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 195-201
    • Kazlauskas, R.J.1
  • 65
    • 33748525883 scopus 로고    scopus 로고
    • Enzyme promiscuity: Evolutionary and mechanistic aspects
    • doi:10.1016/j.cbpa.2006. 08.011
    • Khersonsky, O., Roodveldt, C. & Tawfik, D. S. 2006 Enzyme promiscuity: evolutionary and mechanistic aspects. Curr. Opin. Chem. Biol. 10, 498-508. (doi:10.1016/j.cbpa.2006. 08.011)
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 498-508
    • Khersonsky, O.1    Roodveldt, C.2    Tawfik, D.S.3
  • 66
    • 0034685619 scopus 로고    scopus 로고
    • A breakdown of symmetry in the folding transition state of protein L
    • doi:10.1006/jmbi.2000.3701
    • Kim, D. E., Fisher, C. & Baker, D. 2000 A breakdown of symmetry in the folding transition state of protein L. J. Mol. Biol. 298, 971-984. (doi:10.1006/jmbi.2000.3701)
    • (2000) J. Mol. Biol. , vol.298 , pp. 971-984
    • Kim, D.E.1    Fisher, C.2    Baker, D.3
  • 67
    • 36849138378 scopus 로고
    • The electrostatic influence of substituents on the dissociation constants of organic acids. I
    • doi:10.1063/ 1.1750302
    • Kirkwood, J. G. & Westheimer, F. H. 1938 The electrostatic influence of substituents on the dissociation constants of organic acids. I. J. Chem. Phys. 6, 506-517. (doi:10.1063/ 1.1750302)
    • (1938) J. Chem. Phys. , vol.6 , pp. 506-517
    • Kirkwood, J.G.1    Westheimer, F.H.2
  • 68
    • 0033550206 scopus 로고    scopus 로고
    • De novo protein design. I. in search of stability and specificity
    • doi:10.1006/jmbi.1999.3211
    • Koehl, P. & Levitt, M. 1999a De novo protein design. I. In search of stability and specificity. J. Mol. Biol. 293, 1161-1181. (doi:10.1006/jmbi.1999. 3211)
    • (1999) J. Mol. Biol. , vol.293 , pp. 1161-1181
    • Koehl, P.1    Levitt, M.2
  • 69
    • 0033607205 scopus 로고    scopus 로고
    • Structure-based conformational preferences of amino acids
    • 529. doi:10.1073/pnas.96.22.12524
    • Koehl, P. & Levitt, M. 1999b Structure-based conformational preferences of amino acids. Proc. Natl Acad. Sci. USA 96, 12 524-12 529. (doi:10.1073/pnas.96.22.12524)
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , Issue.12 , pp. 524-612
    • Koehl, P.1    Levitt, M.2
  • 70
    • 0034598938 scopus 로고    scopus 로고
    • Characterization of novel proteins based on known protein structures
    • doi:10.1006/jmbi.1999.3501
    • Koppensteiner, W. A., Lackner, P., Wiederstein, M. & Sippl, M. J. 2000 Characterization of novel proteins based on known protein structures. J. Mol. Biol. 296, 1139-1152. (doi:10.1006/jmbi.1999.3501)
    • (2000) J. Mol. Biol. , vol.296 , pp. 1139-1152
    • Koppensteiner, W.A.1    Lackner, P.2    Wiederstein, M.3    Sippl, M.J.4
  • 72
    • 0141524052 scopus 로고    scopus 로고
    • A de novo redesign of the WW domain
    • doi:10.1110/ps.03190903
    • Kraemer-Pecore, C. M., Lecomte, J. T. & Desjarlais, J. R. 2003 A de novo redesign of the WW domain. Protein Sci. 12, 2194-2205. (doi:10.1110/ps. 03190903)
    • (2003) Protein Sci , vol.12 , pp. 2194-2205
    • Kraemer-Pecore, C.M.1    Lecomte, J.T.2    Desjarlais, J.R.3
  • 73
    • 0041989850 scopus 로고    scopus 로고
    • Challenges in enzyme mechanism and energetics
    • doi:10.1146/annurev.biochem.72. 121801.161617
    • Kraut, D. A., Carroll, K. S. & Herschlag, D. 2003 Challenges in enzyme mechanism and energetics. Annu. Rev. Biochem. 72, 517-571. (doi:10.1146/annurev.biochem.72. 121801.161617)
    • (2003) Annu. Rev. Biochem. , vol.72 , pp. 517-571
    • Kraut, D.A.1    Carroll, K.S.2    Herschlag, D.3
  • 74
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • 388. doi:10.1073/pnas.97.19.10383
    • Kuhlman, B. & Baker, D. 2000 Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 97, 10 383-10 388. (doi:10.1073/pnas.97.19.10383)
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , Issue.10 , pp. 383-410
    • Kuhlman, B.1    Baker, D.2
  • 75
    • 0345306764 scopus 로고    scopus 로고
    • Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
    • DOI 10.1126/science.1089427
    • Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. & Baker, D. 2003 Design of a novel globular protein fold with atomic-level acuracy. Science 302, 1364-1368. (doi:10.1126/science.1089427) (Pubitemid 37452172)
    • (2003) Science , vol.302 , Issue.5649 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard, B.L.5    Baker, D.6
  • 76
    • 18844410540 scopus 로고    scopus 로고
    • Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity
    • doi:10.1093/protein/gzi015
    • Lassila, J., Keeffe, J., Oelschlaeger, P. & Mayo, S. 2005 Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity. Protein Eng. Des. Sel. 18, 161-163. (doi:10.1093/protein/gzi015)
    • (2005) Protein Eng. Des. Sel. , vol.18 , pp. 161-163
    • Lassila, J.1    Keeffe, J.2    Oelschlaeger, P.3    Mayo, S.4
  • 77
    • 33750963095 scopus 로고    scopus 로고
    • Combinatorial methods for small-molecule placement in computational enzyme design
    • 715 doi:10.1073/pnas.0607691103
    • Lassila, J., Privett, H. K., Allen, B. D. & Mayo, S. 2006 Combinatorial methods for small-molecule placement in computational enzyme design. Proc. Natl Acad. Sci. USA 103, 16 710-16 715. (doi:10.1073/pnas. 0607691103)
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , Issue.16 , pp. 710-716
    • Lassila, J.1    Privett, H.K.2    Allen, B.D.3    Mayo, S.4
  • 78
    • 33645218704 scopus 로고    scopus 로고
    • Engineered antibody Fc variants with enhanced effector function
    • doi:10.1073/pnas.0508123103
    • Lazar, G. A. et al. 2006 Engineered antibody Fc variants with enhanced effector function. Proc. Natl Acad. Sci. USA 103, 4005-4010. (doi:10.1073/pnas.0508123103)
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 4005-4010
    • Lazar, G.A.1
  • 79
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • DOI 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
    • Lazaridis, T. & Karplus, M. 1999 Effective energy function for proteins in solution. Proteins 35, 133-152. (doi:10. 1002/(SICI )1097-0134(19990501)35:2<133::AID-PROT 1>3.0.CO;2-N) (Pubitemid 29165128)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.2 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 80
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure prediction
    • doi:10.1016/S0959-440X(00)00063-4
    • Lazaridis, T. & Karplus, M. 2000 Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10, 139-145. (doi:10.1016/S0959-440X(00)00063-4)
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 139-145
    • Lazaridis, T.1    Karplus, M.2
  • 81
    • 0033554840 scopus 로고    scopus 로고
    • Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface
    • DOI 10.1021/bi992271w
    • Loladze, V. V., Ibarra-Molero, B., Sanchez-Ruiz, J. M. & Makhatadze, I. G. 1999 Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface. Biochemistry 38, 16 419-16 423. (doi:10.1021/bi992271w) (Pubitemid 30007493)
    • (1999) Biochemistry , vol.38 , Issue.50 , pp. 16419-16423
    • Loladze, V.V.1    Ibarra-Molero, B.2    Sanchez-Ruiz, J.M.3    Makhatadze, G.I.4
  • 82
    • 0035896029 scopus 로고    scopus 로고
    • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
    • doi:10.1006/jmbi.2000.4424
    • Looger, L. L. & Hellinga, H. W. 2001 Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J. Mol. Biol. 307, 429-445. (doi:10.1006/jmbi.2000.4424)
    • (2001) J. Mol. Biol. , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 83
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • doi:10.1038/ nature01556
    • Looger, L. L., Dwyer, M. A., Smith, J. J. & Hellinga, H. W. 2003 Computational design of receptor and sensor proteins with novel functions. Nature 423, 185-190. (doi:10.1038/ nature01556)
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 84
    • 0345827608 scopus 로고    scopus 로고
    • Sequence determinants of amyloid fibril formation
    • doi:10.1073/pnas.2634884100
    • López de la Paz, M. & Serrano, L. 2004 Sequence determinants of amyloid fibril formation. Proc. Natl Acad. Sci. USA 101, 87-92. (doi:10.1073/pnas.2634884100)
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 87-92
    • De La López Paz, M.1    Serrano, L.2
  • 85
    • 0033214430 scopus 로고    scopus 로고
    • Explicit and implicit water simulations of a b-hairpin peptide
    • Ma, B. & Nussinov, R. 1999 Explicit and implicit water simulations of a b-hairpin peptide. Proteins Struct. Funct. Genet. 37, 73-87.
    • (1999) Proteins Struct. Funct. Genet. , vol.37 , pp. 73-87
    • Ma, B.1    Nussinov, R.2
  • 86
    • 0036663528 scopus 로고    scopus 로고
    • De novo ligand design with explicit water molecules: An application to bacterial neuraminidase
    • doi:10.1023/ A:1021273501447
    • Mancera, R. L. 2002 De novo ligand design with explicit water molecules: an application to bacterial neuraminidase. J. Comput. Aided Mol. Des. 16, 479-499. (doi:10.1023/ A:1021273501447)
    • (2002) J. Comput. Aided Mol. Des. , vol.16 , pp. 479-499
    • Mancera, R.L.1
  • 87
    • 9144240095 scopus 로고
    • DREIDING: A generic force field for molecular simulations
    • doi:10.1021/j100389a010
    • Mayo, S. L., Olafson, B. & Goddard, W. I. 1990 DREIDING: a generic force field for molecular simulations. J. Phys. Chem. 94, 8897-8909. (doi:10.1021/j100389a010)
    • (1990) J. Phys. Chem. , vol.94 , pp. 8897-8909
    • Mayo, S.L.1    Olafson, B.2    Goddard, W.I.3
  • 88
    • 0036667732 scopus 로고    scopus 로고
    • Energy estimation in protein design
    • doi:10.1016/S0959-440X(02)00345-7
    • Mendes, J., Guerois, R. & Serrano, L. 2002 Energy estimation in protein design. Curr. Opin. Struct. Biol. 12, 441-446. (doi:10.1016/S0959- 440X(02)00345-7)
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 441-446
    • Mendes, J.1    Guerois, R.2    Serrano, L.3
  • 89
    • 0035970299 scopus 로고    scopus 로고
    • Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states
    • doi:10. 1006/jmbi.2001.4521
    • Mok, Y. K., Elisseeva, E. L., Davidson, A. R. & Forman-Kay, J. D. 2001 Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states. J. Mol. Biol. 307, 913-928. (doi:10. 1006/jmbi.2001.4521)
    • (2001) J. Mol. Biol. , vol.307 , pp. 913-928
    • Mok, Y.K.1    Elisseeva, E.L.2    Davidson, A.R.3    Forman-Kay, J.D.4
  • 90
    • 0043238060 scopus 로고    scopus 로고
    • Repacking the core of T4 lysozyme by automated design
    • doi:10.1016/S0022-2836(03)00856-8
    • Mooers, B. H. M., Datta, D., Baase, W. A., Zollars, E. S., Mayo, S. L. & Matthews, B. W. 2003 Repacking the core of T4 lysozyme by automated design. J. Mol. Biol. 332, 741-756. (doi:10.1016/S0022-2836(03)00856-8)
    • (2003) J. Mol. Biol. , vol.332 , pp. 741-756
    • Mooers, B.H.M.1    Datta, D.2    Baase, W.A.3    Zollars, E.S.4    Mayo, S.L.5    Matthews, B.W.6
  • 91
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • doi:10.1038/89638
    • Nauli, S., Kuhlman, B. & Baker, D. 2001 Computer-based redesign of a protein folding pathway. Nat. Struct. Mol. Biol. 8, 602-605. (doi:10.1038/89638)
    • (2001) Nat. Struct. Mol. Biol. , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman, B.2    Baker, D.3
  • 92
    • 0033117461 scopus 로고    scopus 로고
    • Catalytic promiscuity and the evolution of new enzymatic activities
    • doi:10.1016/S1074-5521(99)80033-7
    • O'Brien, P. J. & Herschlang, D. 1999 Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6, 91-105. (doi:10.1016/S1074-5521(99)80033-7)
    • (1999) Chem. Biol. , vol.6 , pp. 91-105
    • O'Brien, P.J.1    Herschlang, D.2
  • 93
    • 20444440035 scopus 로고    scopus 로고
    • Hydroxyl groups in the (β)β sandwich of metalleo-β- lactamases favor enzyme activity: A computational protein design study
    • doi:10.1016/j.jmb.2005.04.044
    • Oelschlaeger, P. & Mayo, S. L. 1999 Hydroxyl groups in the (β)β sandwich of metalleo-β-lactamases favor enzyme activity: a computational protein design study. J. Mol. Biol. 350, 395-401. (doi:10.1016/j.jmb.2005.04.044)
    • (1999) J. Mol. Biol. , vol.350 , pp. 395-401
    • Oelschlaeger, P.1    Mayo, S.L.2
  • 95
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • doi:10.1038/372631a0
    • Orengo, C. A., Jones, D. T. & Thornton, J. M. 1994 Protein superfamilies and domain superfolds. Nature 372, 631-634. (doi:10.1038/372631a0)
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 96
    • 0032860932 scopus 로고    scopus 로고
    • Local water bridges and protein conformational stability
    • Petukhov, M., Cregut, D., Soares, C. M. & Serrano, L. 1999 Local water bridges and protein conformational stability. Protein Sci. 8, 1982-1989. (doi:10.1110/ps.8.10.1982) (Pubitemid 29489925)
    • (1999) Protein Science , vol.8 , Issue.10 , pp. 1982-1989
    • Petukhov, M.1    Cregut, D.2    Soares, C.M.3    Serrano, L.4
  • 97
    • 14144256681 scopus 로고    scopus 로고
    • Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
    • doi:10.1016/j.jmb.2004.12.019
    • Pokala, N. & Handel, T. M. 2005 Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J. Mol. Biol. 347, 203-227. (doi:10.1016/j.jmb.2004.12.019)
    • (2005) J. Mol. Biol. , vol.347 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 98
    • 0023812695 scopus 로고
    • Characterization of a helical protein designed from first principles
    • Regan, L. & DeGrado, W. F. 1988 Characterization of a helical protein designed from first principles. Science 241, 976-978. (doi:10.1126/science. 3043666) (Pubitemid 18212972)
    • (1988) Science , vol.241 , Issue.4868 , pp. 976-978
    • Regan, L.1    Degrado, W.F.2
  • 100
    • 34247517470 scopus 로고    scopus 로고
    • Computer-aided design of modular protein devices: Boolean and gene activation
    • doi:10.1088/1478-3975/3/4/007
    • Salis, H. & Kaznessis, Y. N. 2006 Computer-aided design of modular protein devices: Boolean AND gene activation. Phys. Biol. 3, 295-310. (doi:10.1088/1478-3975/3/4/007)
    • (2006) Phys. Biol. , vol.3 , pp. 295-310
    • Salis, H.1    Kaznessis, Y.N.2
  • 101
    • 34247465989 scopus 로고    scopus 로고
    • Engineering modular protein interaction switches by sequence overlap
    • doi:10.1021/ja06 72728
    • Sallee, N. A., Yeh, B. J. & Lim, W. A. 2007 Engineering modular protein interaction switches by sequence overlap. J. Am. Chem. Soc. 129, 4606-4611. (doi:10.1021/ja06 72728)
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 4606-4611
    • Sallee, N.A.1    Yeh, B.J.2    Lim, W.A.3
  • 102
    • 34547605763 scopus 로고    scopus 로고
    • Zinc Finger Targeter (ZiFiT): An engineered zinc finger/target site design tool
    • doi:10.1093/nar/gkm349 (Web server issue)
    • Sander, J. D., Zaback, P., Joung, J. K., Voytas, D. F. & Dobbs, D. 2007 Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res. 35, W599-W605. (doi:10.1093/nar/gkm349) (Web server issue)
    • (2007) Nucleic Acids Res. , vol.35
    • Sander, J.D.1    Zaback, P.2    Joung, J.K.3    Voytas, D.F.4    Dobbs, D.5
  • 103
    • 22544450150 scopus 로고    scopus 로고
    • Prediction of water and metal binding sites and their affinities by using the Fold-X force field
    • 152. doi:10.1073/pnas. 0501980102
    • Schymkowitz, J. W. H., Rousseau, F., Martins, I. C., Ferkinghoff-Borg, J., Stricher, F. & Serrano, L. 2005 Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc. Natl Acad. Sci. USA 102, 10 147-10 152. (doi:10.1073/pnas. 0501980102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.10 , pp. 147-210
    • Schymkowitz, J.W.H.1    Rousseau, F.2    Martins, I.C.3    Ferkinghoff-Borg, J.4    Stricher, F.5    Serrano, L.6
  • 104
    • 58949083856 scopus 로고    scopus 로고
    • Computational protein design with side-chain conformational entropy
    • doi:10.1002/prot.22145
    • Sciretti, D., Bruscolini, P., Alessandro, P., Pretti, M. & Jaramillo, A. 2009 Computational protein design with side-chain conformational entropy. Proteins 74, 176-191. (doi:10.1002/prot.22145)
    • (2009) Proteins , vol.74 , pp. 176-191
    • Sciretti, D.1    Bruscolini, P.2    Alessandro, P.3    Pretti, M.4    Jaramillo, A.5
  • 105
    • 33749343007 scopus 로고    scopus 로고
    • 2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums
    • 973. doi:10.1073/pnas.0606433103
    • 2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums. Proc. Natl Acad. Sci. USA 103, 13 968-13 973. (doi:10.1073/pnas.0606433103)
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , Issue.13 , pp. 968-913
    • Shifman, J.M.1    Choi, M.H.2    Mihalas, S.3    Mayo, S.L.4    Kennedy, M.B.5
  • 106
    • 0035312551 scopus 로고    scopus 로고
    • Macromolecular electrostatics: Continuum models and their growing pains
    • doi:10.1016/S0959-440X(00)00197-4
    • Simonson, T. 2001 Macromolecular electrostatics: continuum models and their growing pains. Curr. Opin. Struct. Biol. 11, 243-252. (doi:10.1016/S0959- 440X(00)00197-4)
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 243-252
    • Simonson, T.1
  • 107
    • 45649084560 scopus 로고    scopus 로고
    • Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
    • doi:10.1016/ j.jmb.2008.05.023
    • Smith, C. A. & Kortemme, T. 2008 Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J. Mol. Biol. 380, 742-756. (doi:10.1016/ j.jmb.2008.05.023)
    • (2008) J. Mol. Biol. , vol.380 , pp. 742-756
    • Smith, C.A.1    Kortemme, T.2
  • 108
    • 33644949935 scopus 로고    scopus 로고
    • Recapitulation and design of protein binding peptide structures and sequences
    • doi:10.1016/j.jmb.2006.01.045
    • Sood, V. & Baker, D. 2006 Recapitulation and design of protein binding peptide structures and sequences. J. Mol. Biol. 357, 917-927. (doi:10.1016/j.jmb.2006.01.045)
    • (2006) J. Mol. Biol. , vol.357 , pp. 917-927
    • Sood, V.1    Baker, D.2
  • 109
    • 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
    • DOI 10.1002/prot.21113
    • Spiegel, K., DeGrado, W. F. & Klein, M. L. 2006 Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations. Proteins 65, 317-333. (doi:10.1002/prot.21113) (Pubitemid 44454107)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.2 , pp. 317-330
    • Spiegel, K.1    De Grado, W.F.2    Klein, M.L.3
  • 110
    • 0031844416 scopus 로고    scopus 로고
    • Pairwise calculation of protein solvent-accessible surface areas
    • doi:10.1016/S1359-0278(98)00036-4
    • Street, A. G. & Mayo, S. L. 1998 Pairwise calculation of protein solvent-accessible surface areas. Fold. Des. 3, 253-259. (doi:10.1016/S1359- 0278(98)00036-4)
    • (1998) Fold. Des. , vol.3 , pp. 253-259
    • Street, A.G.1    Mayo, S.L.2
  • 111
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • Su, A. & Mayo, S. L. 1997 Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6, 1701-1707. (doi:10.1002/pro.5560060810) (Pubitemid 27333072)
    • (1997) Protein Science , vol.6 , Issue.8 , pp. 1701-1707
    • Su, A.1    Mayo, S.L.2
  • 112
    • 57049149647 scopus 로고    scopus 로고
    • Pareto optimization in computational protein design with multiple objectives
    • doi:10.1002/jcc.20981
    • Suárez, M., Tortosa, P., Carrera, J. & Jaramillo, A. 2008 Pareto optimization in computational protein design with multiple objectives. J. Comput. Chem. 29, 2704-2711. (doi:10.1002/jcc.20981)
    • (2008) J. Comput. Chem. , vol.29 , pp. 2704-2711
    • Suárez, M.1    Tortosa, P.2    Carrera, J.3    Jaramillo, A.4
  • 115
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • doi:10.1016/j.jmb.2003.08.057
    • Tian, W. D. & Skolnick, J. 2003 How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol. 333, 863-882. (doi:10.1016/j.jmb.2003.08.057)
    • (2003) J. Mol. Biol. , vol.333 , pp. 863-882
    • Tian, W.D.1    Skolnick, J.2
  • 116
    • 33846102955 scopus 로고    scopus 로고
    • Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function
    • doi:10.1073/pnas. 0609647103
    • Treynor, T., Vizcarra, C. L., Nedelcu, D. & Mayo, S. L. 2007 Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc. Natl Acad. Sci. USA 104, 48-53. (doi:10.1073/pnas. 0609647103)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 48-53
    • Treynor, T.1    Vizcarra, C.L.2    Nedelcu, D.3    Mayo, S.L.4
  • 117
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side chain conformations
    • Tuffery, P., Etchebest, C., Hazout, S. & Lavery, R. 1991 A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 8, 1267-1289.
    • (1991) J. Biomol. Struct. Dyn. , vol.8 , pp. 1267-1289
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 118
    • 33750014560 scopus 로고    scopus 로고
    • Solvated docking: Introducing water into the modelling of biomolecular complexes
    • doi:10. 1093/bioinformatics/btl395
    • van Dijk, A. D. J. & Bonvin, A. M. J. J. 2006 Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics 22, 2340-2347. (doi:10. 1093/bioinformatics/btl395)
    • (2006) Bioinformatics , vol.22 , pp. 2340-2347
    • Van Dijk, A.D.J.1    Bonvin, A.M.J.J.2
  • 119
    • 42149085208 scopus 로고    scopus 로고
    • An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
    • doi:10.1002/jcc.20878
    • Vizcarra, C. L., Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C. & Mayo, S. L. 2008 An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J. Comput. Chem. 29, 1153-1162. (doi:10.1002/jcc.20878)
    • (2008) J. Comput. Chem. , vol.29 , pp. 1153-1162
    • Vizcarra, C.L.1    Zhang, N.2    Marshall, S.A.3    Wingreen, N.S.4    Zeng, C.5    Mayo, S.L.6
  • 120
    • 0035957360 scopus 로고    scopus 로고
    • Computational method to reduce the search space for directed protein evolution
    • doi:10.1073/pnas.051614498
    • Voigt, C. A., Mayo, S. L., Arnold, F. H. & Wang, Z. G. 2001 Computational method to reduce the search space for directed protein evolution. Proc. Natl Acad. Sci. USA 98, 3778-3783. (doi:10.1073/pnas.051614498)
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 3778-3783
    • Voigt, C.A.1    Mayo, S.L.2    Arnold, F.H.3    Wang, Z.G.4
  • 122
    • 0034682869 scopus 로고    scopus 로고
    • Automatic protein design with all atom force-fields by exact and heuristic optimization
    • doi:10.1006/ jmbi.2000.3984
    • Wernisch, L., Hery, S. & Wodak, S. 2000 Automatic protein design with all atom force-fields by exact and heuristic optimization. J. Mol. Biol. 301, 713-736. (doi:10.1006/ jmbi.2000.3984)
    • (2000) J. Mol. Biol. , vol.301 , pp. 713-736
    • Wernisch, L.1    Hery, S.2    Wodak, S.3
  • 123
    • 0027411034 scopus 로고
    • Protein folding in the absence of the solvent ordering contribution to the hydrophobic interaction
    • doi:10.1006/ jmbi.1993.1049
    • Woolfson, D. N., Cooper, A., Harding, M. M., Williams, D. H. & Evans, P. A. 1993 Protein folding in the absence of the solvent ordering contribution to the hydrophobic interaction. J. Mol. Biol. 229, 502-511. (doi:10.1006/ jmbi.1993.1049)
    • (1993) J. Mol. Biol. , vol.229 , pp. 502-511
    • Woolfson, D.N.1    Cooper, A.2    Harding, M.M.3    Williams, D.H.4    Evans, P.A.5
  • 125
    • 58549091879 scopus 로고    scopus 로고
    • Computational design of calmodulin mutants with up to 900-fold increase in binding specificity
    • doi:10.1016/j.jmb.2008.09.053
    • Yosef, E., Politi, R., Choi, M. H. & Shifman, J. M. 2009 Computational design of calmodulin mutants with up to 900-fold increase in binding specificity. J. Mol. Biol. 385, 1470-1480. (doi:10.1016/j.jmb.2008.09. 053)
    • (2009) J. Mol. Biol. , vol.385 , pp. 1470-1480
    • Yosef, E.1    Politi, R.2    Choi, M.H.3    Shifman, J.M.4
  • 127
    • 33845977740 scopus 로고    scopus 로고
    • On side-chain conformational entropy of proteins
    • doi:10. 1371/journal.pcbi.0020168
    • Zhang, J. & Liu, J. S. 2006 On side-chain conformational entropy of proteins. PLoS Comput. Biol. 2, e168. (doi:10. 1371/journal.pcbi.0020168)
    • (2006) PLoS Comput. Biol. , vol.2
    • Zhang, J.1    Liu, J.S.2
  • 128
    • 4143101125 scopus 로고    scopus 로고
    • Guiding the search for a protein's maximum rate of folding
    • doi:10.1016/j.chemphys.2004.05.008
    • Zhu, Y., Fu, X., Wang, T., Tamura, A., Takada, S., Saven, J. G. & Gai, F. 2004 Guiding the search for a protein's maximum rate of folding. Chem. Phys. 307, 99-109. (doi:10.1016/j.chemphys.2004.05.008)
    • (2004) Chem. Phys. , vol.307 , pp. 99-109
    • Zhu, Y.1    Fu, X.2    Wang, T.3    Tamura, A.4    Takada, S.5    Saven, J.G.6    Gai, F.7


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