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Volumn 96, Issue 9, 2009, Pages 3483-3494

A free-energy approach for all-atom protein simulation

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HUMAN IMMUNODEFICIENCY VIRUS PROTEIN; PEPTIDE; PROTEIN; HOMEODOMAIN PROTEIN;

EID: 67650354848     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.12.3921     Document Type: Article
Times cited : (25)

References (74)
  • 1
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker, D., and A. Sali. 2001. Protein structure prediction and structural genomics. Science. 294:93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 3
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley, P., K. M. S. Misura, and D. Baker. 2005. Toward high-resolution de novo structure prediction for small proteins. Science. 309:1868-1871.
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 4
    • 34547617731 scopus 로고    scopus 로고
    • Characterization of protein-folding pathways by reduced-space modeling
    • Kmiecik, S., and A. Kolinski. 2007. Characterization of protein-folding pathways by reduced-space modeling. Proc. Natl. Acad. Sci. USA. 104:12330-12335.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 12330-12335
    • Kmiecik, S.1    Kolinski, A.2
  • 5
    • 30044442528 scopus 로고    scopus 로고
    • High-resolution protein folding with a transferable potential
    • Hubner, I. A., E. J. Deeds, and E. I. Shakhnovich. 2005. High-resolution protein folding with a transferable potential. Proc. Natl. Acad. Sci. USA. 102:18914-18919.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 18914-18919
    • Hubner, I.A.1    Deeds, E.J.2    Shakhnovich, E.I.3
  • 6
    • 33748604047 scopus 로고    scopus 로고
    • PROFASI: A Monte Carlo simulation package for protein folding and aggregation
    • Irbäck, A., and S. Mohanty. 2006. PROFASI: a Monte Carlo simulation package for protein folding and aggregation. J. Comput. Chem. 27:1548-1555.
    • (2006) J. Comput. Chem , vol.27 , pp. 1548-1555
    • Irbäck, A.1    Mohanty, S.2
  • 7
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling, C., B. Strockbine, and A. E. Roitberg. 2002. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124:11258-11259.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 8
    • 1642570290 scopus 로고    scopus 로고
    • Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy
    • Snow, C. D., L. Qiu, D. Du, F. Gai, S. J. Hagen, et al. 2004. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc. Natl. Acad. Sci. USA. 101:4077-4082.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 4077-4082
    • Snow, C.D.1    Qiu, L.2    Du, D.3    Gai, F.4    Hagen, S.J.5
  • 9
    • 1442287309 scopus 로고    scopus 로고
    • Comparisons of force fields for proteins by generalized-ensemble simulations
    • Yoda, T., Y. Sugita, and Y. Okamoto. 2004. Comparisons of force fields for proteins by generalized-ensemble simulations. Chem. Phys. Lett. 386:460-467.
    • (2004) Chem. Phys. Lett , vol.386 , pp. 460-467
    • Yoda, T.1    Sugita, Y.2    Okamoto, Y.3
  • 10
    • 33846314325 scopus 로고    scopus 로고
    • Force field effects on a β-sheet protein domain structure in thermal unfolding simulations
    • Wang, T., and R. C. Wade. 2006. Force field effects on a β-sheet protein domain structure in thermal unfolding simulations. J. Chem. Theory Comput. 2:140-148.
    • (2006) J. Chem. Theory Comput , vol.2 , pp. 140-148
    • Wang, T.1    Wade, R.C.2
  • 11
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple AMBER force fields and development of improved protein backbone parameters
    • Hornak, V., R. Abel, A. Okur, B. Strockbine, A. Roitberg, et al. 2006. Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins. Struct. Funct. Bioinform. 65:712-725.
    • (2006) Proteins. Struct. Funct. Bioinform , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5
  • 12
    • 11244302065 scopus 로고    scopus 로고
    • An all-atom force field for tertiary structure prediction of helical proteins
    • Herges, T., and W. Wenzel. 2004. An all-atom force field for tertiary structure prediction of helical proteins. Biophys. J. 87:3100-3109.
    • (2004) Biophys. J , vol.87 , pp. 3100-3109
    • Herges, T.1    Wenzel, W.2
  • 13
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C. B. 1973. Principles that govern the folding of protein chains. Science. 181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 16
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate x-ray and near-native folds from well-constructed decoys
    • Park, B., and M. Levitt. 1996. Energy functions that discriminate x-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:367-392.
    • (1996) J. Mol. Biol , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 18
    • 9744236584 scopus 로고    scopus 로고
    • Ensemble of transition states for two-state protein folding from the eigenvectors of rate matrices
    • Berezhkovskii, A., and A. Szabo. 2004. Ensemble of transition states for two-state protein folding from the eigenvectors of rate matrices. J. Chem. Phys. 121:9186-9187.
    • (2004) J. Chem. Phys , vol.121 , pp. 9186-9187
    • Berezhkovskii, A.1    Szabo, A.2
  • 19
    • 18744366086 scopus 로고    scopus 로고
    • Chemical theory and computation special feature: Protein folding pathways from replica exchange simulations and a kinetic network model
    • Andrec, M., A. K. Felts, E. Gallicchio, and R. M. Levy. 2005. Chemical theory and computation special feature: protein folding pathways from replica exchange simulations and a kinetic network model. Proc. Natl. Acad. Sci. USA. 102:6801-6806.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6801-6806
    • Andrec, M.1    Felts, A.K.2    Gallicchio, E.3    Levy, R.M.4
  • 20
    • 33645408056 scopus 로고    scopus 로고
    • Balancing solvation and intramolecular interactions: Toward a consistent Generalized Born force field
    • Chen, J., W. Im, and C. L. Brooks. 2006. Balancing solvation and intramolecular interactions: toward a consistent Generalized Born force field. J. Am. Chem. Soc. 128:3728-3736.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 3728-3736
    • Chen, J.1    Im, W.2    Brooks, C.L.3
  • 21
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replica-exchange simulations of "Trp-cage" miniproteins
    • Pitera, J. W., and W. Swope. 2003. Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. Proc. Natl. Acad. Sci. USA. 100:7587-7592.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 22
    • 33749665952 scopus 로고    scopus 로고
    • Basin hopping simulations for all-atom protein folding
    • Verma, A., A. Schug, K. H. Lee, and W. Wenzel. 2006. Basin hopping simulations for all-atom protein folding. J. Chem. Phys. 124:44515.
    • (2006) J. Chem. Phys , vol.124 , pp. 44515
    • Verma, A.1    Schug, A.2    Lee, K.H.3    Wenzel, W.4
  • 23
    • 33744816177 scopus 로고    scopus 로고
    • An evolutionary strategy for all-atom folding of the sixty amino acid bacterial ribosomal protein L20
    • Schug, A., and W. Wenzel. 2006. An evolutionary strategy for all-atom folding of the sixty amino acid bacterial ribosomal protein L20. Biophys. J. 90:4273-4280.
    • (2006) Biophys. J , vol.90 , pp. 4273-4280
    • Schug, A.1    Wenzel, W.2
  • 24
    • 35948929892 scopus 로고    scopus 로고
    • All-atom de novo protein folding with a scalable evolutionary algorithm
    • Verma, A., S. M. Gopal, J. S. Oh, K. H. Lee, and W. Wenzel. 2007. All-atom de novo protein folding with a scalable evolutionary algorithm. J. Comput. Chem. 28:2552-2558.
    • (2007) J. Comput. Chem , vol.28 , pp. 2552-2558
    • Verma, A.1    Gopal, S.M.2    Oh, J.S.3    Lee, K.H.4    Wenzel, W.5
  • 25
    • 18144364015 scopus 로고    scopus 로고
    • In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field
    • Herges, T., and W. Wenzel. 2005. In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field. Phys. Rev. Lett. 94:018101.
    • (2005) Phys. Rev. Lett , vol.94 , pp. 018101
    • Herges, T.1    Wenzel, W.2
  • 26
    • 4544246504 scopus 로고    scopus 로고
    • Exploration of the free-energy surface of a three-helix peptide with stochastic optimization methods
    • Herges, T., A. Schug, and W. Wenzel. 2004. Exploration of the free-energy surface of a three-helix peptide with stochastic optimization methods. Int. J. Quantum Chem. 99:854-863.
    • (2004) Int. J. Quantum Chem , vol.99 , pp. 854-863
    • Herges, T.1    Schug, A.2    Wenzel, W.3
  • 27
    • 21144456638 scopus 로고    scopus 로고
    • Protein structure prediction with stochastic optimization methods: Folding and misfolding the villin headpiece
    • L. Gavrilova, V. Kumar, Y. Mun, and C. J. K. Tan, et al, editors. Springer, New York
    • Herges, T., A. Schug, and W. Wenzel. 2004. Protein structure prediction with stochastic optimization methods: folding and misfolding the villin headpiece. In Lecture Notes in Computer Science. A. Lagana, M. L. Gavrilova, V. Kumar, Y. Mun, and C. J. K. Tan, et al., editors. Springer, New York 454-464.
    • (2004) Lecture Notes in Computer Science. A. Lagana , vol.1000 , pp. 454-464
    • Herges, T.1    Schug, A.2    Wenzel, W.3
  • 28
    • 0642285282 scopus 로고    scopus 로고
    • Reproducible protein folding with the stochastic tunneling method
    • Schug, A., T. Herges, and W. Wenzel. 2003. Reproducible protein folding with the stochastic tunneling method. Phys. Rev. Lett. 91:158102.
    • (2003) Phys. Rev. Lett , vol.91 , pp. 158102
    • Schug, A.1    Herges, T.2    Wenzel, W.3
  • 29
    • 3142735955 scopus 로고    scopus 로고
    • All-atom folding of the Trp-cage protein with an adaptive parallel tempering method
    • Schug, A., and W. Wenzel. 2004. All-atom folding of the Trp-cage protein with an adaptive parallel tempering method. Europhys. Lett. 67:307-313.
    • (2004) Europhys. Lett , vol.67 , pp. 307-313
    • Schug, A.1    Wenzel, W.2
  • 30
    • 10344222927 scopus 로고    scopus 로고
    • All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method
    • Schug, A., T. Herges, and W. Wenzel. 2004. All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method. Proteins. Struct. Funct. Bioinform. 57:792-798.
    • (2004) Proteins. Struct. Funct. Bioinform , vol.57 , pp. 792-798
    • Schug, A.1    Herges, T.2    Wenzel, W.3
  • 31
    • 11244338015 scopus 로고    scopus 로고
    • Predictive in silico all-atom folding of a four-helix protein with a free-energy model
    • Schug, A., and W. Wenzel. 2004. Predictive in silico all-atom folding of a four-helix protein with a free-energy model. J. Am. Chem. Soc. 126:16736-16737.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 16736-16737
    • Schug, A.1    Wenzel, W.2
  • 32
    • 17044382925 scopus 로고    scopus 로고
    • Free-energy landscape of the villin headpiece in an all-atom force field
    • Herges, T., and W. Wenzel. 2005. Free-energy landscape of the villin headpiece in an all-atom force field. Structure. 13:661-668.
    • (2005) Structure , vol.13 , pp. 661-668
    • Herges, T.1    Wenzel, W.2
  • 33
    • 0034718553 scopus 로고    scopus 로고
    • Folding simulations of a three-stranded antiparallel β-sheet peptide
    • Ferrara, P., and A. Caflisch. 2000. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. USA. 97:10780-10785.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10780-10785
    • Ferrara, P.1    Caflisch, A.2
  • 34
    • 17844386576 scopus 로고    scopus 로고
    • Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide
    • Cavalli, A., M. Vendruscolo, and E. Paci. 2005. Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide. Biophys. J. 88:3158-3166.
    • (2005) Biophys. J , vol.88 , pp. 3158-3166
    • Cavalli, A.1    Vendruscolo, M.2    Paci, E.3
  • 35
    • 2642586516 scopus 로고    scopus 로고
    • Folding thermodynamics of three b-sheet peptides: A model study
    • Irbäck, A., and F. Sjunnesson. 2004. Folding thermodynamics of three b-sheet peptides: a model study. Proteins. Struct. Funct. Bioinform. 56:110-116.
    • (2004) Proteins. Struct. Funct. Bioinform , vol.56 , pp. 110-116
    • Irbäck, A.1    Sjunnesson, F.2
  • 36
    • 2942625637 scopus 로고    scopus 로고
    • Design and characterization of helical peptides that inhibit the E6 protein of papillomavirus
    • Liu, Y., Z. Liu, E. Androphy, J. Chen, and J. D. Baleja. 2004. Design and characterization of helical peptides that inhibit the E6 protein of papillomavirus. Biochemistry. 43:7421-7431.
    • (2004) Biochemistry , vol.43 , pp. 7421-7431
    • Liu, Y.1    Liu, Z.2    Androphy, E.3    Chen, J.4    Baleja, J.D.5
  • 37
    • 0028032397 scopus 로고    scopus 로고
    • Clarke,N.D., C. R.Kissinger, J.Desjarlais, G. L.Gilliland, andC.O. Pabo. 1994. Structural studies of the engrailed homeodomain. Protein Sci. 3:1779-1787.
    • Clarke,N.D., C. R.Kissinger, J.Desjarlais, G. L.Gilliland, andC.O. Pabo. 1994. Structural studies of the engrailed homeodomain. Protein Sci. 3:1779-1787.
  • 38
    • 0037136192 scopus 로고    scopus 로고
    • Comparison of stochastic optimization methods for receptor-ligand docking
    • Merlitz, H., and W. Wenzel. 2002. Comparison of stochastic optimization methods for receptor-ligand docking. Chem. Phys. Lett. 362:271-277.
    • (2002) Chem. Phys. Lett , vol.362 , pp. 271-277
    • Merlitz, H.1    Wenzel, W.2
  • 39
    • 0001487498 scopus 로고    scopus 로고
    • Stochastic tunneling approach for global optimization of complex potential energy landscapes
    • Wenzel, W., and K. Hamacher. 1999. Stochastic tunneling approach for global optimization of complex potential energy landscapes. Phys. Rev. Lett. 82:3003-3007.
    • (1999) Phys. Rev. Lett , vol.82 , pp. 3003-3007
    • Wenzel, W.1    Hamacher, K.2
  • 40
    • 10344222927 scopus 로고    scopus 로고
    • All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method
    • Schug, A., T. Herges, and W. Wenzel. 2004. All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method. Proteins. 57:792-798.
    • (2004) Proteins , vol.57 , pp. 792-798
    • Schug, A.1    Herges, T.2    Wenzel, W.3
  • 41
    • 85031363525 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 42
    • 21444457267 scopus 로고    scopus 로고
    • Energy landscape paving simulations of the Trp-cage protein
    • Schug, A., W. Wenzel, and U. H. Hansmann. 2005. Energy landscape paving simulations of the Trp-cage protein. J. Chem. Phys. 122:194711.
    • (2005) J. Chem. Phys , vol.122 , pp. 194711
    • Schug, A.1    Wenzel, W.2    Hansmann, U.H.3
  • 43
    • 29144432368 scopus 로고    scopus 로고
    • Comparison of stochastic optimization methods for all-atom folding of the Trp-cage protein
    • Schug, A., T. Herges, A. Verma, K. H. Lee, and W. Wenzel. 2005. Comparison of stochastic optimization methods for all-atom folding of the Trp-cage protein. ChemPhysChem. 6:2640-2646.
    • (2005) ChemPhysChem , vol.6 , pp. 2640-2646
    • Schug, A.1    Herges, T.2    Verma, A.3    Lee, K.H.4    Wenzel, W.5
  • 44
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., C. D. Gelatt, and M. P. Vecchi. 1983. Optimization by simulated annealing. Science. 220:671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 46
    • 85031364807 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 47
    • 0035956886 scopus 로고    scopus 로고
    • Recent improvements in prediction of protein structure by global optimization of a potential energy function
    • Pillardy, J., C. Czaplewski, A. Liwo, J. Lee, D. R. Ripoll, et al. 2001. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA. 98:2329-2333.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 2329-2333
    • Pillardy, J.1    Czaplewski, C.2    Liwo, A.3    Lee, J.4    Ripoll, D.R.5
  • 48
    • 0026723852 scopus 로고
    • Use of a potential of mean force to analyze free energy contributions in protein folding
    • Avbelj, F. 1992. Use of a potential of mean force to analyze free energy contributions in protein folding. Biochemistry. 31:6290-6297.
    • (1992) Biochemistry , vol.31 , pp. 6290-6297
    • Avbelj, F.1
  • 49
    • 0028960071 scopus 로고
    • Role of electrostatic screening in determining protein main chain conformational preferences
    • Avbelj, F., and J. Moult. 1995. Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry. 34:755-764.
    • (1995) Biochemistry , vol.34 , pp. 755-764
    • Avbelj, F.1    Moult, J.2
  • 50
    • 0000545402 scopus 로고
    • A comparative study of the simulated-annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [Met]-encephalin
    • Nayeem, A., J. Vila, and H. A. Scheraga. 1991. A comparative study of the simulated-annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [Met]-encephalin. J. Comput. Chem. 12:594-605.
    • (1991) J. Comput. Chem , vol.12 , pp. 594-605
    • Nayeem, A.1    Vila, J.2    Scheraga, H.A.3
  • 51
    • 0000560869 scopus 로고    scopus 로고
    • Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms
    • Wales, D. J., and J. P. K. Doye. 1997. Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J. Phys. Chem. A. 101:5111-5116.
    • (1997) J. Phys. Chem. A , vol.101 , pp. 5111-5116
    • Wales, D.J.1    Doye, J.P.K.2
  • 52
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan, R., and M. Totrov. 1994. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:983-1002.
    • (1994) J. Mol. Biol , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 53
    • 10844286223 scopus 로고    scopus 로고
    • Effect of salt bridges on the energy landscape of a model protein
    • Wales, D. J., and P. E. J. Dewsbury. 2004. Effect of salt bridges on the energy landscape of a model protein. J. Chem. Phys. 121:10284-10290.
    • (2004) J. Chem. Phys , vol.121 , pp. 10284-10290
    • Wales, D.J.1    Dewsbury, P.E.J.2
  • 54
    • 85031359225 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 55
    • 0001553991 scopus 로고    scopus 로고
    • Bouncing towards the optimum: Improving the results of Monte Carlo optimization algorithms
    • Schneider, J., I. Morgenstern, and J. M. Singer. 1998. Bouncing towards the optimum: improving the results of Monte Carlo optimization algorithms. Phys. Rev. E. 58:5085-5095.
    • (1998) Phys. Rev. E , vol.58 , pp. 5085-5095
    • Schneider, J.1    Morgenstern, I.2    Singer, J.M.3
  • 56
    • 85031354022 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 57
    • 0000504484 scopus 로고    scopus 로고
    • Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure
    • Abagyan, R. A., and M. Totrov. 1999. Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. J. Comput. Phys. 151:402-421.
    • (1999) J. Comput. Phys , vol.151 , pp. 402-421
    • Abagyan, R.A.1    Totrov, M.2
  • 58
    • 19644387091 scopus 로고    scopus 로고
    • On the orientation of the backbone dipoles in native folds
    • Ripoll, D. R., J. A. Vila, and H. A. Scheraga. 2005. On the orientation of the backbone dipoles in native folds. Proc. Natl. Acad. Sci. USA. 102:7559-7564.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 7559-7564
    • Ripoll, D.R.1    Vila, J.A.2    Scheraga, H.A.3
  • 59
  • 60
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala, R., and J. Moult. 1998. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275:895-916.
    • (1998) J. Mol. Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 61
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou, H., and Y. Zhou. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11:2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 62
    • 0035253047 scopus 로고    scopus 로고
    • Zinc finger proteins: New insights into structural and functional diversity
    • Laity, J. H., B. M. Lee, and P. E. Wright. 2001. Zinc finger proteins: new insights into structural and functional diversity. Curr. Opin. Struct. Biol. 11:39-46.
    • (2001) Curr. Opin. Struct. Biol , vol.11 , pp. 39-46
    • Laity, J.H.1    Lee, B.M.2    Wright, P.E.3
  • 63
    • 0024341072 scopus 로고
    • Three-dimensional solution structure of a single zinc finger DNA-binding domain
    • Lee, M. S., G. P. Gippert, K. V. Soman, D. A. Case, and P. E. Wright. 1989. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science. 245:635-637.
    • (1989) Science , vol.245 , pp. 635-637
    • Lee, M.S.1    Gippert, G.P.2    Soman, K.V.3    Case, D.A.4    Wright, P.E.5
  • 64
    • 0033930952 scopus 로고    scopus 로고
    • Advances in zinc finger engineering
    • Choo, Y., and M. Isalan. 2000. Advances in zinc finger engineering. Curr. Opin. Struct. Biol. 10:411-416.
    • (2000) Curr. Opin. Struct. Biol , vol.10 , pp. 411-416
    • Choo, Y.1    Isalan, M.2
  • 65
    • 0037456298 scopus 로고    scopus 로고
    • The complete folding pathway of a protein from nanoseconds to microseconds
    • Mayor, U., N. R. Guydosh, C. M. Johnson, J. G. Grossmann, S. Sato, et al. 2003. The complete folding pathway of a protein from nanoseconds to microseconds. Nature. 421:863-867.
    • (2003) Nature , vol.421 , pp. 863-867
    • Mayor, U.1    Guydosh, N.R.2    Johnson, C.M.3    Grossmann, J.G.4    Sato, S.5
  • 67
    • 85031367638 scopus 로고    scopus 로고
    • PhD Thesis, FZKA, Institut für Nanotechnologie, Institut für Wissenschaftliches Rechnen. Forschungszentrum Karlsruhe/Universitat Dortmund, Germany
    • Verma, A. 2007. Development and application of a free energy force field for all atom protein folding. PhD Thesis, FZKA 7334. Institut für Nanotechnologie, Institut für Wissenschaftliches Rechnen. Forschungszentrum Karlsruhe/Universitat Dortmund, Germany.
    • (2007) Development and application of a free energy force field for all atom protein folding , pp. 7334
    • Verma, A.1
  • 68
    • 43849093505 scopus 로고    scopus 로고
    • Ten-microsecond MD simulation of a fast-folding WW domain
    • Freddolino, P. L., F. Liu, M. H. Gruebele, and K. Schulten. 2008. Ten-microsecond MD simulation of a fast-folding WW domain. Biophys. J. 94:L75-L77.
    • (2008) Biophys. J , vol.94
    • Freddolino, P.L.1    Liu, F.2    Gruebele, M.H.3    Schulten, K.4
  • 69
    • 0344304436 scopus 로고    scopus 로고
    • Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures
    • Vila, J. A., D. R. Ripoll, and H. A. Scheraga. 2003. Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc. Natl. Acad. Sci. USA. 100:14812-14816.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 14812-14816
    • Vila, J.A.1    Ripoll, D.R.2    Scheraga, H.A.3
  • 70
    • 33748248896 scopus 로고    scopus 로고
    • Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the villin headpiece
    • Jayachandran, G., V. Vishal, and V. S. Pande. 2006. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J. Chem. Phys. 124:164902.
    • (2006) J. Chem. Phys , vol.124 , pp. 164902
    • Jayachandran, G.1    Vishal, V.2    Pande, V.S.3
  • 71
    • 0024406542 scopus 로고
    • A molecular dynamics analysis of protein structural elements
    • Post, C. B., C. M. Dobson, and M. Karplus. 1989. A molecular dynamics analysis of protein structural elements. Proteins Struct. Funct. Genet. 5:337-354.
    • (1989) Proteins Struct. Funct. Genet , vol.5 , pp. 337-354
    • Post, C.B.1    Dobson, C.M.2    Karplus, M.3
  • 73
    • 30144445192 scopus 로고    scopus 로고
    • Side-chain entropy effects on protein secondary structure formation
    • Chellgren, B. W., and T. P. Creamer. 2006. Side-chain entropy effects on protein secondary structure formation. Proteins. Struct. Funct. Bioinform. 62:411-420.
    • (2006) Proteins. Struct. Funct. Bioinform , vol.62 , pp. 411-420
    • Chellgren, B.W.1    Creamer, T.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.