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Volumn 6, Issue 11, 2010, Pages

Exploring the universe of protein structures beyond the protein data bank

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN FOLDING;

EID: 78649636970     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000957     Document Type: Article
Times cited : (61)

References (39)
  • 1
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • Chothia C, Finkelstein A (1990) The classification and origins of protein folding patterns. Annu Rev Biochem 59: 1007-1039.
    • (1990) Annu Rev Biochem , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.2
  • 2
    • 0027122748 scopus 로고
    • Proteins - 1000 families for the molecular biologist
    • Chothia C (1992) Proteins - 1000 families for the molecular biologist. Nature 357: 543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 3
    • 0025363984 scopus 로고
    • Deciphering the message in protein sequences - tolerance to amino-acid substitutions
    • Bowie J, Reidhaarolson J, Lim W, Sauer R (1990) Deciphering the message in protein sequences - tolerance to amino-acid substitutions. Science 247: 1306-1310.
    • (1990) Science , vol.247 , pp. 1306-1310
    • Bowie, J.1    Reidhaarolson, J.2    Lim, W.3    Sauer, R.4
  • 4
    • 0027255479 scopus 로고
    • Structural and genetic analysis of protein stability
    • Matthews B (1993) Structural and genetic analysis of protein stability. Annu Rev Biochem 62: 139-160.
    • (1993) Annu Rev Biochem , vol.62 , pp. 139-160
    • Matthews, B.1
  • 5
    • 0029952910 scopus 로고    scopus 로고
    • Symmetry and the energy landscapes of biomolecules
    • Wolynes P (1996) Symmetry and the energy landscapes of biomolecules. Proc Natl Acad Sci USA 93: 14249-14255.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 14249-14255
    • Wolynes, P.1
  • 6
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • Munoz V, Eaton W (1999) A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 96: 11311-11316.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 11311-11316
    • Munoz, V.1    Eaton, W.2
  • 7
    • 0033613131 scopus 로고    scopus 로고
    • A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
    • Galzitskaya O, Finkelstein A (1999) A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci USA 96: 11299-11304.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 11299-11304
    • Galzitskaya, O.1    Finkelstein, A.2
  • 8
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker D (2000) A surprising simplicity to protein folding. Nature 405: 39-42.
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 9
    • 0141480054 scopus 로고    scopus 로고
    • Funnel sculpting for in silico assembly of secondary structure elements of proteins
    • Fain B, Levitt M (2003) Funnel sculpting for in silico assembly of secondary structure elements of proteins. Proc Natl Acad Sci USA 100: 10700-10705.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10700-10705
    • Fain, B.1    Levitt, M.2
  • 11
    • 0026490069 scopus 로고
    • Poly(L-alanine) as a universal reference material for understanding protein energies and structures
    • Headgordon T, Stillinger F, Wright M, Gay D (1992) Poly(L-alanine) as a universal reference material for understanding protein energies and structures. Proc Natl Acad Sci USA 89: 11513-11517.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 11513-11517
    • Headgordon, T.1    Stillinger, F.2    Wright, M.3    Gay, D.4
  • 13
    • 33646466620 scopus 로고    scopus 로고
    • Common attributes of native-state structures of proteins, disordered proteins, and amyloid
    • Hoang T, Marsella L, Trovato A, Seno F, Banavar J, et al. (2006) Common attributes of native-state structures of proteins, disordered proteins, and amyloid. Proc Natl Acad Sci USA 103: 6883-6888.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 6883-6888
    • Hoang, T.1    Marsella, L.2    Trovato, A.3    Seno, F.4    Banavar, J.5
  • 15
  • 17
    • 44449093098 scopus 로고    scopus 로고
    • Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
    • Huang X, Bowman GR, Pande VS (2008) Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. J Chem Phys 128: 205106.
    • (2008) J Chem Phys , vol.128 , pp. 205106
    • Huang, X.1    Bowman, G.R.2    Pande, V.S.3
  • 18
    • 34249071886 scopus 로고    scopus 로고
    • A bias-exchange approach to protein folding
    • Piana S, Laio A (2007) A bias-exchange approach to protein folding. J Phys Chem B 111: 4553-4559.
    • (2007) J Phys Chem B , vol.111 , pp. 4553-4559
    • Piana, S.1    Laio, A.2
  • 19
    • 0030777303 scopus 로고    scopus 로고
    • CATH - a hierarchic classification of protein domain structures
    • Orengo C, Michie A, Jones S, Jones D, Swindells M, et al. (1997) CATH - a hierarchic classification of protein domain structures. Structure 5: 1093-1108.
    • (1997) Structure , vol.5 , pp. 1093-1108
    • Orengo, C.1    Michie, A.2    Jones, S.3    Jones, D.4    Swindells, M.5
  • 20
    • 0242663237 scopus 로고    scopus 로고
    • A pointcharge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, et al. (2003) A pointcharge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24: 1999-2012.
    • (2003) J Comput Chem , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.M.5
  • 21
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • Laskowski R, Rullmann J, MacArthur M, Kaptein R, Thornton J (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477-486.
    • (1996) J Biomol NMR , vol.8 , pp. 477-486
    • Laskowski, R.1    Rullmann, J.2    Macarthur, M.3    Kaptein, R.4    Thornton, J.5
  • 22
    • 12944249776 scopus 로고
    • Discussion of solution for best rotation to relate 2 sets of vectors
    • Kabsch W (1978) Discussion of solution for best rotation to relate 2 sets of vectors. Acta Crystallogr A 34: 827-828.
    • (1978) Acta Crystallogr A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 23
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 24
    • 70349461173 scopus 로고    scopus 로고
    • The continuity of protein structure space is an intrinsic property of proteins
    • Skolnick J, Arakaki AK, Lee SY, Brylinski M (2009) The continuity of protein structure space is an intrinsic property of proteins. Proc Natl Acad Sci USA 106: 15690-15695.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 15690-15695
    • Skolnick, J.1    Arakaki, A.K.2    Lee, S.Y.3    Brylinski, M.4
  • 25
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K, Simons K, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277: 985-994.
    • (1998) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.1    Simons, K.2    Baker, D.3
  • 26
    • 33846426123 scopus 로고    scopus 로고
    • From never born proteins to minimal living cells: Two projects in synthetic biology
    • Luisi PL, Chiarabelli C, Stano P (2006) From never born proteins to minimal living cells: Two projects in synthetic biology. Orig Life Evol Biosph 36: 605-616.
    • (2006) Orig Life Evol Biosph , vol.36 , pp. 605-616
    • Luisi, P.L.1    Chiarabelli, C.2    Stano, P.3
  • 27
    • 33748541979 scopus 로고    scopus 로고
    • Investigation of de novo totally random biosequences Part II On the folding frequency in a totally random library of de novo proteins obtained by phage display
    • Chiarabelli C, Vrijbloed JW, De Lucrezia D, Thomas RM, Stano P, et al. (2006) Investigation of de novo totally random biosequences Part II On the folding frequency in a totally random library of de novo proteins obtained by phage display. Chem Biodivers 3: 840-859.
    • (2006) Chem Biodivers , vol.3 , pp. 840-859
    • Chiarabelli, C.1    Vrijbloed, J.W.2    de Lucrezia, D.3    Thomas, R.M.4    Stano, P.5
  • 28
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid, and human disease
    • Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75: 333-366.
    • (2006) Annu Rev Biochem , vol.75 , pp. 333-366
    • Chiti, F.1    Dobson, C.M.2
  • 29
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with rosetta
    • Rohl C, Strauss C, Chivian D, Baker D (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55: 656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.1    Strauss, C.2    Chivian, D.3    Baker, D.4
  • 30
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
    • (2001) J Mol Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 31
    • 36548999391 scopus 로고    scopus 로고
    • Predicting the effect of a point mutation on a protein fold: The villin and advillin headpieces and their Pro62Ala mutants
    • Piana S, Laio A, Marinelli F, Van Troys M, Bourry D, et al. (2008) Predicting the effect of a point mutation on a protein fold: The villin and advillin headpieces and their Pro62Ala mutants. J Mol Biol 375: 460-470.
    • (2008) J Mol Biol , vol.375 , pp. 460-470
    • Piana, S.1    Laio, A.2    Marinelli, F.3    van Troys, M.4    Bourry, D.5
  • 32
    • 0031578972 scopus 로고    scopus 로고
    • Parallel tempering algorithm for conformational studies of biological molecules
    • Hansmann UHE (1997) Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 281: 140.
    • (1997) Chem Phys Lett , vol.281 , pp. 140
    • Hansmann, U.H.E.1
  • 34
    • 73349098763 scopus 로고    scopus 로고
    • A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1
    • Pietrucci F, Laio A (2009) A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1. J Chem Theory Comput 5: 2197-2201.
    • (2009) J Chem Theory Comput , vol.5 , pp. 2197-2201
    • Pietrucci, F.1    Laio, A.2
  • 35
    • 69049084558 scopus 로고    scopus 로고
    • Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations
    • Pietrucci F, Marinelli F, Carloni P, Laio A (2009) Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations. J Am Chem Soc 131: 11811-11818.
    • (2009) J Am Chem Soc , vol.131 , pp. 11811-11818
    • Pietrucci, F.1    Marinelli, F.2    Carloni, P.3    Laio, A.4
  • 36
    • 77749316142 scopus 로고    scopus 로고
    • Optimizing the performace of Bias Exchange Metadynamics for protein folding
    • Cossio P, Marinelli F, Laio A, Pietrucci F (2010) Optimizing the performace of Bias Exchange Metadynamics for protein folding. J Phys Chem B 114: 3259-3265.
    • (2010) J Phys Chem B , vol.114 , pp. 3259-3265
    • Cossio, P.1    Marinelli, F.2    Laio, A.3    Pietrucci, F.4
  • 37
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure - patternrecognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure - patternrecognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 38
    • 0018782641 scopus 로고
    • Hierarchic organization of domains in globular proteins
    • Rose G (1979) Hierarchic organization of domains in globular proteins. J Mol Biol 134: 447-470.
    • (1979) J Mol Biol , vol.134 , pp. 447-470
    • Rose, G.1


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