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Volumn 87, Issue 4, 2004, Pages 2240-2246

How does averaging affect protein structure comparison on the ensemble level?

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA HELIX; ARTICLE; COMPARATIVE STUDY; MATHEMATICAL ANALYSIS; PROTEIN STRUCTURE; STATISTICAL SIGNIFICANCE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; EVALUATION; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; REPRODUCIBILITY; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL; VALIDATION STUDY;

EID: 16644374796     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.042184     Document Type: Article
Times cited : (26)

References (27)
  • 1
    • 48749148224 scopus 로고
    • Rattle: A "velocity" version of the Shake algorithm for molecular dynamics calculations
    • Andersen, H. C. 1983. Rattle: a "velocity" version of the Shake algorithm for molecular dynamics calculations. J. Comp. Phys. 52:24-34.
    • (1983) J. Comp. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 5
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 6
    • 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
  • 7
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • Fersht, A. R., and V. Daggett. 2002. Protein folding and unfolding at atomic resolution. Cell. 108:573-582.
    • (2002) Cell , vol.108 , pp. 573-582
    • Fersht, A.R.1    Daggett, V.2
  • 8
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
    • Garcia, A. E., and J. N. Onuchic. 2003. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. USA. 100:13898-13903.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13898-13903
    • Garcia, A.E.1    Onuchic, J.N.2
  • 9
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a beta hairpin in explicit solvent
    • Garcia, A. E., and K. Y. Sanbonmatsu. 2001. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins. 42:345-354.
    • (2001) Proteins , vol.42 , pp. 345-354
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 10
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins: Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins: energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1666-1671.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1666-1671
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 11
    • 0038054301 scopus 로고    scopus 로고
    • Experimental tests of villin subdomain folding simulations
    • Kubelka, J., W. A. Eaton, and J. Hofrichter. 2003. Experimental tests of villin subdomain folding simulations. J. Mol. Biol. 329:625-630.
    • (2003) J. Mol. Biol. , vol.329 , pp. 625-630
    • Kubelka, J.1    Eaton, W.A.2    Hofrichter, J.3
  • 12
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • Mayor, U., C. M. Johnson, V. Daggett, and A. R. Fersht. 2000. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. USA. 97:13518-13522.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 13
    • 0031058410 scopus 로고    scopus 로고
    • NMR structure of the 35-residue villin headpiece subdomain
    • McKnight, C. J., P. T. Matsudaira, and P. S. Kim. 1997. NMR structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4:180-184.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 180-184
    • McKnight, C.J.1    Matsudaira, P.T.2    Kim, P.S.3
  • 14
    • 0036401140 scopus 로고    scopus 로고
    • Toward a taxonomy of the denatured state: Small angle scattering studies of unfolded proteins
    • Millett, I. S., S. Doniach, and K. W. Plaxco. 2002. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv. Protein Chem. 62:241-262.
    • (2002) Adv. Protein Chem. , vol.62 , pp. 241-262
    • Millett, I.S.1    Doniach, S.2    Plaxco, K.W.3
  • 15
    • 0037478676 scopus 로고    scopus 로고
    • Analysis of the distributed computing approach applied to the folding of a small beta peptide
    • Paci, E., A. Cavalli, M. Vendruscolo, and A. Caflisch. 2003. Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc. Natl. Acad. Sci. USA. 100:8217-8222.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 8217-8222
    • Paci, E.1    Cavalli, A.2    Vendruscolo, M.3    Caflisch, A.4
  • 17
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
    • Qiu, D., P. S. Shenkin, F. P. Hollinger, and W. C. Still. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. 101:3005-3014.
    • (1997) J. Phys. Chem. , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 18
    • 0034743155 scopus 로고    scopus 로고
    • From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
    • Shea, J. E., and C. L. Brooks, III. 2001. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52:499-535.
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 499-535
    • Shea, J.E.1    Brooks III, C.L.2
  • 19
    • 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
  • 20
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow, C. D., H. Nguyen, V. S. Pande, and M. Gruebele. 2002a. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420:102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, H.2    Pande, V.S.3    Gruebele, M.4
  • 21
    • 0037065310 scopus 로고    scopus 로고
    • The Tip cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
    • Snow, C. D., B. Zagrovic, and V. S. Pande. 2002b. The Tip cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J. Am. Chem. Soc. 124:14548-14549.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 14548-14549
    • Snow, C.D.1    Zagrovic, B.2    Pande, V.S.3
  • 22
    • 0141990950 scopus 로고    scopus 로고
    • Effect of gatekeepers on the early folding kinetics of a model beta-barrel protein
    • Stoycheva, A. D., J. N. Onuchic, and C. L. Brooks, III. 2003. Effect of gatekeepers on the early folding kinetics of a model beta-barrel protein. J. Chem. Phys. 119:5722-5729.
    • (2003) J. Chem. Phys. , vol.119 , pp. 5722-5729
    • Stoycheva, A.D.1    Onuchic, J.N.2    Brooks III, C.L.3
  • 23
    • 0035910479 scopus 로고    scopus 로고
    • The key to solving the protein-folding problem lies in an accurate description of the denatured state
    • van Gunsteren, W. F., R. Burgi, C. Peter, and X. Daura. 2001. The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew. Chem. Int. Ed. Engl. 40:352-355.
    • (2001) Angew. Chem. Int. Ed. Engl. , vol.40 , pp. 352-355
    • Van Gunsteren, W.F.1    Burgi, R.2    Peter, C.3    Daura, X.4
  • 24
    • 0242407127 scopus 로고    scopus 로고
    • Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like features
    • Zagrovic, B., and V. S. Pande. 2003. Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like features. Nat. Struct. Biol. 10:955-961.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 955-961
    • Zagrovic, B.1    Pande, V.S.2
  • 25
    • 0036394906 scopus 로고    scopus 로고
    • Native-like mean structure in the unfolded ensemble of small proteins
    • Zagrovic, B., C. Snow, S. Khaliq, M. Shirts, and V. Pande. 2002a. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323:153-164.
    • (2002) J. Mol. Biol. , vol.323 , pp. 153-164
    • Zagrovic, B.1    Snow, C.2    Khaliq, S.3    Shirts, M.4    Pande, V.5
  • 26
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic, B., C. D. Snow, M. R. Shirts, and V. S. Pande. 2002b. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323:927-937.
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 27
    • 0035850758 scopus 로고    scopus 로고
    • Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
    • Zagrovic, B., E. J. Sorin, and V. Pande. 2001. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313:151-169.
    • (2001) J. Mol. Biol. , vol.313 , pp. 151-169
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.