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Volumn 98, Issue 10, 2010, Pages 2299-2308

Protein thermostability calculations using alchemical free energy simulations

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EID: 77952786853     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.01.056     Document Type: Article
Times cited : (33)

References (66)
  • 1
    • 4143131151 scopus 로고    scopus 로고
    • De novo design of catalytic proteins
    • Kaplan, J., and W. F. DeGrado. 2004. De novo design of catalytic proteins. Proc, Natl. Acad, Sci. USA. 101:11566-11570.
    • (2004) Proc, Natl. Acad, Sci. USA. , vol.101 , pp. 11566-11570
    • Kaplan, J.1    Degrado, W.F.2
  • 2
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design, of retro-aldol enzymes
    • Jiang, L., E. A. Althoff, ..., D. Baker. 2008. De novo computational design, of retro-aldol enzymes. Science. 319:1387-1391.
    • (2008) Science. , vol.319 , pp. 1387-1391
    • Jiang, L.1    Althoff, E.A.2    Baker, D.3
  • 3
    • 43449098518 scopus 로고    scopus 로고
    • Kemp elimination catalysts by computational enzyme design
    • Röthlisberger, D., O. Khersonsky, ..., D. Baker. 2008. Kemp elimination catalysts by computational enzyme design. Nature. 453:190-195.
    • (2008) Nature. , vol.453 , pp. 190-195
    • Röthlisberger, D.1    Khersonsky, O.2    Baker, D.3
  • 4
    • 33646352962 scopus 로고    scopus 로고
    • Potent antibody therapeutics by design
    • Carter, P. J. 2006. Potent antibody therapeutics by design. Nat. Rev. Immunol. 6:343-357.
    • (2006) Nat. Rev. Immunol. , vol.6 , pp. 343-357
    • Carter, P.J.1
  • 5
    • 67749111952 scopus 로고    scopus 로고
    • Design of therapeutic proteins with enhanced stability
    • Chennamsetty, N., V. Voynov, ..., B. L. Trout. 2009. Design of therapeutic proteins with enhanced stability. Proc. Natl. Acad. Sci. USA, 106:11937-11942.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 11937-11942
    • Chennamsetty, N.1    Voynov, V.2    Trout, B.L.3
  • 6
    • 33750317306 scopus 로고    scopus 로고
    • Bioinformaticsdriven, rational engineering of protein thermostability
    • Ditursi, M. K., S. J. Kwon, ..., J. S. Dordick. 2006. Bioinformaticsdriven, rational engineering of protein thermostability. Protein Eng. Des. Sel. 19:517-524.
    • (2006) Protein Eng. Des. Sel. , vol.19 , pp. 517-524
    • Ditursi, M.K.1    Kwon, S.J.2    Dordick, J.S.3
  • 7
    • 18244373419 scopus 로고    scopus 로고
    • Computational thermostabilization of an enzyme
    • Korkegian, A., M. E. Black, ..., B. L. Stoddard. 2005. Computational thermostabilization of an enzyme. Science. 308:857-860.
    • (2005) Science. , vol.308 , pp. 857-860
    • Korkegian, A.1    Black, M.E.2    Stoddard, B.L.3
  • 8
    • 0034017055 scopus 로고    scopus 로고
    • Factors enhancing protein, thermostability
    • Kumar, S., C. J. Tsai, and R. Nussinov. 2000. Factors enhancing protein, thermostability. Protein. Eng. 13:179-191.
    • (2000) Protein. Eng. , vol.13 , pp. 179-191
    • Kumar, S.1    Tsai, C.J.2    Nussinov, R.3
  • 9
    • 0037338175 scopus 로고    scopus 로고
    • Rational design and engineering of therapeutic proteins
    • Marshall, S. A., G. A. Lazar, ..., J. R. Desjarlais. 2003. Rational design and engineering of therapeutic proteins. DrugDiscov. Today. 8:212-221.
    • (2003) DrugDiscov. Today. , vol.8 , pp. 212-221
    • Marshall, S.A.1    Lazar, G.A.2    Desjarlais, J.R.3
  • 10
    • 1642464839 scopus 로고    scopus 로고
    • Protein structure prediction using Rosetta
    • Rohl, C. A., C. E. Strauss, ..., D. Baker. 2004. Protein structure prediction using Rosetta. Methods Enzymol. 383:66-93.
    • (2004) Methods Enzymol. , vol.383 , pp. 66-93
    • Rohl, C.A.1    Strauss, C.E.2    Baker, D.3
  • 11
    • 23144436398 scopus 로고    scopus 로고
    • The FoldX web server: An online force field
    • (Web Server issue)
    • Schymkowitz, J., J. Borg, L. Serrano. 2005. The FoldX web server: an online force field. Nucleic Acids Res. 33(Web Server issue): W382-W388.
    • (2005) Nucleic Acids Res. , vol.33
    • Schymkowitz, J.1    Borg, J.2    Serrano, L.3
  • 12
    • 58149247893 scopus 로고    scopus 로고
    • Predicting free energy changes using structural ensembles
    • Benedix, A., C. M. Becker,..., R. A. Böckmann. 2009. Predicting free energy changes using structural ensembles. Nat. Methods. 6:3-4.
    • (2009) Nat. Methods. , vol.6 , pp. 3-4
    • Benedix, A.1    Becker, C.M.2    Böckmann, R.A.3
  • 13
    • 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
    • Pokala, N., and T. M. Handel. 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.
    • (2005) J. Mol. Biol. , vol.347 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 14
    • 23144461249 scopus 로고    scopus 로고
    • I-MUTANT2.0: Predicting stability changes upon mutation from the protein, sequence or structure
    • (Web Server issue)
    • Capriotti, E., P. Fariselli, and R. Casadio. 2005. I-MUTANT2.0: predicting stability changes upon mutation from the protein, sequence or structure. Nucleic Acids Res. 33(Web Server issue):W306-W310.
    • (2005) Nucleic Acids Res. , vol.33
    • Capriotti, E.1    Fariselli, P.2    Casadio, R.3
  • 15
    • 0035843136 scopus 로고    scopus 로고
    • Combinatorial and computational challenges for biocatalyst design
    • Arnold, F. H. 2001. Combinatorial and computational challenges for biocatalyst design. Nature, 409:253-257.
    • (2001) Nature , vol.409 , pp. 253-257
    • Arnold, F.H.1
  • 16
    • 62649153772 scopus 로고    scopus 로고
    • Computational structure-based redesign of enzyme activity
    • Chen, C. Y., I. Georgiev, ..., B. R. Donald. 2009. Computational structure-based redesign of enzyme activity. Proc. Natl. Acad. Sci. USA. 106:3764-3769.
    • (2009) Proc. Natl. Acad. Sci. USA. , vol.106 , pp. 3764-3769
    • Chen, C.Y.1    Georgiev, I.2    Donald, B.R.3
  • 17
    • 0035843122 scopus 로고    scopus 로고
    • Enzymes for chemical synthesis
    • Koeller, K. M., and C. H. Wong. 2001. Enzymes for chemical synthesis. Nature. 409:232-240.
    • (2001) Nature. , vol.409 , pp. 232-240
    • Koeller, K.M.1    Wong, C.H.2
  • 18
    • 0035843170 scopus 로고    scopus 로고
    • Industrial biocatalysis today and tomorrow
    • Schmid, A., J. S. Dordick, ..., B. Witholt. 2001. Industrial biocatalysis today and tomorrow. Nature. 409:258-268.
    • (2001) Nature. , vol.409 , pp. 258-268
    • Schmid, A.1    Dordick, J.S.2    Witholt, B.3
  • 19
    • 34250872269 scopus 로고    scopus 로고
    • Minimalist active-site redesign; teaching old enzymes new tricks
    • Toscano, M., K. Woycechowsky, and D. Hilvert. 2007. Minimalist active-site redesign; teaching old enzymes new tricks. Angew. Chem. 46:3212-3236.
    • (2007) Angew. Chem. , vol.46 , pp. 3212-3236
    • Toscano, M.1    Woycechowsky, K.2    Hilvert, D.3
  • 20
    • 0035843132 scopus 로고    scopus 로고
    • Enabling the chemistry of life
    • Walsh, C. 2001. Enabling the chemistry of life. Nature. 409:226-231.
    • (2001) Nature. , vol.409 , pp. 226-231
    • Walsh, C.1
  • 21
    • 0035843166 scopus 로고    scopus 로고
    • Improving enzymes by using them in organic solvents
    • Klibanov, A. M. 2001, Improving enzymes by using them in organic solvents. Nature. 409:241-246.
    • (2001) Nature. , vol.409 , pp. 241-246
    • Klibanov, A.M.1
  • 23
    • 74549207309 scopus 로고    scopus 로고
    • Assessing computational methods for predicting protein, stability upon, mutation: Good on average but not in. the details
    • Potapov, V., M. Cohen, and G. Schreiber. 2009. Assessing computational methods for predicting protein, stability upon, mutation: good on average but not in. the details. Protein Eng. Des. Sel. 22:553-560.
    • (2009) Protein Eng. Des. Sel. , vol.22 , pp. 553-560
    • Potapov, V.1    Cohen, M.2    Schreiber, G.3
  • 24
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen, W. 2004. The many roles of computation in drug discovery. Sci. STKE. 303:1813-1818.
    • (2004) Sci. STKE. , vol.303 , pp. 1813-1818
    • Jorgensen, W.1
  • 25
    • 67650495212 scopus 로고    scopus 로고
    • Lambda-dynamics free energy simulation methods
    • Knight, J. L., and C. L. Brooks, 3rd. 2009. Lambda-dynamics free energy simulation methods. J. Comput. Chem. 30:1692-1700.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1692-1700
    • Knight, J.L.1    Brooks III, C.L.2
  • 26
    • 0004504539 scopus 로고
    • Monte Carlo simulation of differences in free energies of hydration
    • Jorgensen, W., and C. Ravimohan. 1985. Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 83: 3050-3054.
    • (1985) J. Chem. Phys. , vol.83 , pp. 3050-3054
    • Jorgensen, W.1    Ravimohan, C.2
  • 27
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge, D. L., and F. M. DiCapua. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-492.
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431-492
    • Beveridge, D.L.1    Dicapua, F.M.2
  • 28
    • 36849122972 scopus 로고
    • High-temperature equation, of state by a perturbation method. 1. Nonpolar gases
    • Zwanzig, R. W. 1954. High-temperature equation, of state by a perturbation method. 1. Nonpolar gases. J. Chem. Phys. 22:1420-1426.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 29
    • 0001563899 scopus 로고
    • Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations
    • Straatsma, T., and H. Berendsen. 1988. Free energy of ionic hydration: analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations. J. Chem. Phys. 89:5876-5886.
    • (1988) J. Chem. Phys. , vol.89 , pp. 5876-5886
    • Straatsma, T.1    Berendsen, H.2
  • 30
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy difference
    • Jarzynski, C. 1997. Nonequilibrium equality for free energy difference. Phys. Rev. Lett. 78:2690-2693.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 31
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
    • Jarzynski, C. 1997. Equilibrium free-energy differences from nonequilibrium measurements: a master-equation approach. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 56:5018-5035.
    • (1997) Phys. Rev. e Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics , vol.56 , pp. 5018-5035
    • Jarzynski, C.1
  • 32
    • 0032023968 scopus 로고    scopus 로고
    • Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems
    • Crooks, G. 1998. Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems. J. Stat. Phys. 90:1481-1487.
    • (1998) J. Stat. Phys. , vol.90 , pp. 1481-1487
    • Crooks, G.1
  • 33
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple AMBER force fields and development of improved protein backbone parameters
    • Hornak, V., R. Abel, ..., C. Simmerling. 2006. Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins: Struct. Funct. Bioinf. 65:712-725.
    • (2006) Proteins: Struct. Funct. Bioinf. , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Simmerling, C.3
  • 34
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B., C. Kutzner, ..., E. Lindahl. 2008. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4:435-447.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Lindahl, E.3
  • 36
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L., J. Chandrasekhar, ..., M. L. Klein. 1983.Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Klein, M.L.3
  • 37
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • Parrinello, M., and A. Rahman. 1981. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52: 7182-7190.
    • (1981) J. Appl. Phys. , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 38
    • 33645961739 scopus 로고
    • A smooth particle mesh Ewald potential
    • Essmann, U., L. Perera, ..., L. G. Pedersen. 1995. A smooth particle mesh Ewald potential. J. Chem. Phys. 103:8577-8592.
    • (1995) J. Chem. Phys. , vol.103 , pp. 8577-8592
    • Essmann, U.1    Perera, L.2    Pedersen, L.G.3
  • 39
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
    • Miyamoto, S., and P. A. Kollman. 1992. SETTLE: an analytical version of the SHAKE and RATTLE Algorithms for Rigid Water Models. J. Comput. Chem. 13:952-962.
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 40
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B., H. Bekker, ..., J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Fraaije, J.G.E.M.3
  • 41
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • 4.1, Bussi, G., D. Donadio, and M. Parrinello. 2007. Canonical sampling through velocity rescaling. J. Chem. Phys. 126:014101.
    • (2007) J. Chem. Phys. , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 42
    • 59849121675 scopus 로고    scopus 로고
    • Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes
    • Goette, M., and H. Grubmüller. 2008. Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J. Comput. Chem. 30:447-456.
    • (2008) J. Comput. Chem. , vol.30 , pp. 447-456
    • Goette, M.1    Grubmüller, H.2
  • 43
    • 0034669841 scopus 로고    scopus 로고
    • Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
    • Pitera, J., P. Kollman., and M. Center. 2000. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins: Struct. Funct. Bioinf 41:385-397.
    • (2000) Proteins: Struct. Funct. Bioinf , vol.41 , pp. 385-397
    • Pitera, J.1    Kollman, P.2    Center, M.3
  • 44
    • 33644874615 scopus 로고    scopus 로고
    • ProTherm and ProNIT: Thennodynamic databases for proteins and protein-nucleic acid interactions
    • (Database issue)
    • Kumar, M. D., K. A. Bava, ..., A. Sarai. 2006. ProTherm and ProNIT: thennodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res. 34(Database issue):D204-D206.
    • (2006) Nucleic Acids Res. , vol.34
    • Kumar, M.D.1    Bava, K.A.2    Sarai, A.3
  • 45
    • 0026674251 scopus 로고
    • Alpha-helix stability in proteins. II. Factors that influence stability at an internal position
    • Horovitz, A., J. M. Matthews, and A. R. Fersht. 1992. Alpha-helix stability in proteins. II. Factors that influence stability at an internal position. J. Mol. Biol. 227:560-568.
    • (1992) J. Mol. Biol. , vol.227 , pp. 560-568
    • Horovitz, A.1    Matthews, J.M.2    Fersht, A.R.3
  • 46
    • 0024295240 scopus 로고
    • Contribution of hydrophobic interactions to protein stability
    • Kellis, Jr., J. T., K. Nyberg, ..., A. R. Fersht. 1988. Contribution of hydrophobic interactions to protein stability. Nature. 333:784-786.
    • (1988) Nature. , vol.333 , pp. 784-786
    • Kellis Jr., J.T.1    Nyberg, K.2    Fersht, A.R.3
  • 48
    • 0024358426 scopus 로고
    • Mapping the transition state and pathway of protein folding by protein engineering
    • Matouschek, A., J. T. Kellis, Jr., ..., A. R. Fersht. 1989. Mapping the transition state and pathway of protein folding by protein engineering. Nature. 340:122-126.
    • (1989) Nature. , vol.340 , pp. 122-126
    • Matouschek, A.1    Kellis Jr., J.T.2    Fersht, A.R.3
  • 49
    • 0028168139 scopus 로고
    • Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions
    • Matouschek, A., J. Matthews, ..., A. Fersht. 1994. Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions. Protein Eng. Des. Sel. 7:1089-1095.
    • (1994) Protein Eng. Des. Sel. , vol.7 , pp. 1089-1095
    • Matouschek, A.1    Matthews, J.2    Fersht, A.3
  • 50
    • 0028983182 scopus 로고
    • a values of the denatured state are on average 0.4 units lower than those of model compounds
    • a values of the denatured state are on average 0.4 units lower than those of model compounds. Biochemistry. 34:9424-9433.
    • (1995) Biochemistry. , vol.34 , pp. 9424-9433
    • Oliveberg, M.1    Arcus, V.L.2    Fersht, A.R.3
  • 51
    • 0029943662 scopus 로고    scopus 로고
    • New approach to the study of transient protein conformations: The formation of a semiburied salt link in. the folding pathway of barnase
    • Oliveberg, M., and A. R. Fersht. 1996. New approach to the study of transient protein conformations: the formation of a semiburied salt link in. the folding pathway of barnase. Biochemistry. 35:6795-6805.
    • (1996) Biochemistry. , vol.35 , pp. 6795-6805
    • Oliveberg, M.1    Fersht, A.R.2
  • 53
    • 0025756736 scopus 로고
    • Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles
    • Serrano, L., M. Bycroft, and A. R. Fersht. 1991. Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles. J. Mol. Biol. 218:465-475.
    • (1991) J. Mol. Biol. , vol.218 , pp. 465-475
    • Serrano, L.1    Bycroft, M.2    Fersht, A.R.3
  • 54
    • 0027441807 scopus 로고
    • Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability
    • Serrano, L., A. G. Day, and A. R. Fersht. 1993. Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J. Mol. Biol. 233:305-312.
    • (1993) J. Mol. Biol. , vol.233 , pp. 305-312
    • Serrano, L.1    Day, A.G.2    Fersht, A.R.3
  • 55
    • 0024972479 scopus 로고
    • Capping and α-helix stability
    • Serrano, L., and A. R. Fersht. 1989. Capping and α-helix stability. Nature. 342:296-299.
    • (1989) Nature. , vol.342 , pp. 296-299
    • Serrano, L.1    Fersht, A.R.2
  • 56
    • 0025093185 scopus 로고
    • Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles
    • Serrano, L., A. Horovitz, ..., A. R. Fersht. 1990. Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles. Biochemistry. 29:9343-9352.
    • (1990) Biochemistry. , vol.29 , pp. 9343-9352
    • Serrano, L.1    Horovitz, A.2    Fersht, A.R.3
  • 57
    • 0026553768 scopus 로고
    • The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
    • Serrano, L., J. T. Kellis, Jr, ...., A. R. Fersht. 1992. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224:783-804.
    • (1992) J. Mol. Biol. , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis Jr., J.T.2    Fersht, A.R.3
  • 58
    • 0026709329 scopus 로고
    • Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces
    • Serrano, L., J. Sancho, ..., A. R. Fersht. 1992. Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces. J. Mol. Biol. 227:544-559.
    • (1992) J. Mol. Biol. , vol.227 , pp. 544-559
    • Serrano, L.1    Sancho, J.2    Fersht, A.R.3
  • 59
    • 0024553005 scopus 로고
    • Effect of the substitution Ala-GIy at each of five residue positions in the C-peptide helix
    • Strehlow, K. G., and R. L. Baldwin. 1989. Effect of the substitution Ala-GIy at each of five residue positions in the C-peptide helix. Biochemistry. 28:2.130-2133.
    • (1989) Biochemistry. , vol.28 , pp. 2130-2133
    • Strehlow, K.G.1    Baldwin, R.L.2
  • 60
    • 1642307617 scopus 로고    scopus 로고
    • The folding pathway of barnase: The rate-limiting transition state and a hidden intermediate under native conditions
    • Vu, N. D., H. Feng, and Y. Bai. 2004. The folding pathway of barnase: the rate-limiting transition state and a hidden intermediate under native conditions. Biochemistry. 43:3346-3356.
    • (2004) Biochemistry. , vol.43 , pp. 3346-3356
    • Vu, N.D.1    Feng, H.2    Bai, Y.3
  • 61
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers. , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 62
    • 35748982413 scopus 로고    scopus 로고
    • Geometry-based sampling of conformational transitions in proteins
    • Seeliger, D., J. Haas, and B. L. de Groot. 2007. Geometry-based sampling of conformational transitions in proteins. Structure. 15: 1482-1492.
    • (2007) Structure. , vol.15 , pp. 1482-1492
    • Seeliger, D.1    Haas, J.2    De Groot, B.L.3
  • 63
    • 33745614865 scopus 로고    scopus 로고
    • Dramatic performance enhancements for the FASTER optimization algorithm
    • Allen, B. D., and S. L. Mayo. 2006. Dramatic performance enhancements for the FASTER optimization algorithm. J. Comput. Chem. 27: 1071-1075.
    • (2006) J. Comput. Chem. , vol.27 , pp. 1071-1075
    • Allen, B.D.1    Mayo, S.L.2
  • 64
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • Dunbrack, Jr., R. L., and M. Karplus. 1993. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230:543-574.
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 65
    • 33749578940 scopus 로고    scopus 로고
    • Statistical, potential for assessment and prediction, of protein, structures
    • Shen, M. Y., and A. Sali. 2006. Statistical, potential for assessment and prediction, of protein, structures. Protein Sci. 15:2507-2524.
    • (2006) Protein Sci. , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 66
    • 46449132707 scopus 로고    scopus 로고
    • Specific interactions for ab initio folding of protein terminal regions with secondary structures
    • Yang, Y., and Y. Zhou. 2008. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins: Struct. Funct. Bioinf 72:793-803.
    • (2008) Proteins: Struct. Funct. Bioinf , vol.72 , pp. 793-803
    • Yang, Y.1    Zhou, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.