메뉴 건너뛰기




Volumn 7, Issue 44, 2010, Pages 397-408

Analysis of a complete DNA - protein affinity landscape

Author keywords

Allophycocyanin; Aptamer; NK landscape; Tness landscapes

Indexed keywords

BIOCHIPS; BIOLOGY; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PROTEINS;

EID: 76049090891     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2009.0193     Document Type: Article
Times cited : (54)

References (29)
  • 1
    • 0346659780 scopus 로고    scopus 로고
    • Fitness distance correlation analysis: An instructive counterexample
    • East Lansing, MI, 19-23 July, San Francisco, CA: Morgan Kaufmann
    • Altenberg, L. 1997 Fitness distance correlation analysis: an instructive counterexample. In Proc. 7th Int. Conf. on Genetic Algorithms, East Lansing, MI, 19-23 July 1997, pp. 57-64. San Francisco, CA: Morgan Kaufmann.
    • (1997) Proc. 7th Int. Conf. on Genetic Algorithms , pp. 57-64
    • Altenberg, L.1
  • 2
    • 67649982744 scopus 로고    scopus 로고
    • Diversity and complexity in DNA recognition by transcription factors
    • doi:10.1126/science.1162327
    • Badis, G. et al. 2009 Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723. (doi:10.1126/science.1162327)
    • (2009) Science , vol.324 , pp. 1720-1723
    • Badis, G.1
  • 3
    • 0030596731 scopus 로고    scopus 로고
    • Approximate scaling properties of RNA free energy landscapes
    • doi:10.1006/jtbi.1996. 0132
    • Baskaran, S., Stadler, P. F. & Schuster, P. 1996 Approximate scaling properties of RNA free energy landscapes. J. Theoret. Biol. 181, 299-310. (doi:10.1006/jtbi.1996. 0132)
    • (1996) J. Theoret. Biol , vol.181 , pp. 299-310
    • Baskaran, S.1    Stadler, P.F.2    Schuster, P.3
  • 4
    • 0002460716 scopus 로고
    • Epistasis variance: A viewpoint on GAhardness
    • ed. G. J. E. Rawlins, San Mateo, CA: Morgan Kaufmann
    • Davidor, Y. 1991 Epistasis variance: a viewpoint on GAhardness. In Foundations of genetic algorithms (ed. G. J. E. Rawlins). San Mateo, CA: Morgan Kaufmann.
    • (1991) Foundations of genetic algorithms
    • Davidor, Y.1
  • 5
    • 4243861085 scopus 로고
    • Random-energy model: An exactly solvable model of disordered systems
    • doi:10.1103/PhysRevB. 24.2613
    • Derrida, B. 1981 Random-energy model: an exactly solvable model of disordered systems. Phys. Rev. B 24, 2613. (doi:10.1103/PhysRevB. 24.2613)
    • (1981) Phys. Rev. B , vol.24 , pp. 2613
    • Derrida, B.1
  • 6
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for double-stranded nucleic acids
    • doi:10.1529/biophysj.103.020743
    • Dimitrov, R. A. & Zuker, M. 2004 Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J. 87, 215-226. (doi:10.1529/biophysj.103.020743)
    • (2004) Biophys. J , vol.87 , pp. 215-226
    • Dimitrov, R.A.1    Zuker, M.2
  • 7
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • doi:10.1016/S0022-5193(87)80029-2
    • Ellington, A. D. & Szostak, J. W. 1990 In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822. (doi:10.1016/S0022-5193(87)80029-2)
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 8
    • 84943817322 scopus 로고
    • Error detecting and error correcting codes
    • Hamming, R. W. 1950 Error detecting and error correcting codes. Bell Syst. Tech. 29, 147-160.
    • (1950) Bell Syst. Tech , vol.29 , pp. 147-160
    • Hamming, R.W.1
  • 9
    • 0003155122 scopus 로고
    • Fitness distance correlation as a measure of problem dif.culty for genetic algorithms
    • Pittsburgh, PA, 15-19 July, San Francisco, CA: Morgan Kaufmann
    • Jones, T. & Forrest, S. 1995 Fitness distance correlation as a measure of problem dif.culty for genetic algorithms. In Proc. 6th Int. Conf. on Genetic Algorithms, Pittsburgh, PA, 15-19 July 1995, pp. 184-192. San Francisco, CA: Morgan Kaufmann.
    • (1995) Proc. 6th Int. Conf. on Genetic Algorithms , pp. 184-192
    • Jones, T.1    Forrest, S.2
  • 10
    • 85020834404 scopus 로고    scopus 로고
    • Kallel, L., Naudts, B. & Reeves, C. R. 2001 Properties of .tness functions and search landscapes. In Theoretical aspects of evolutionary computing, (eds L. Kallel, B. Naudts & A. Rogers). pp. 175-206. Berlin, Germany: Springer-Verlag.
    • Kallel, L., Naudts, B. & Reeves, C. R. 2001 Properties of .tness functions and search landscapes. In Theoretical aspects of evolutionary computing, (eds L. Kallel, B. Naudts & A. Rogers). pp. 175-206. Berlin, Germany: Springer-Verlag.
  • 11
    • 38049048268 scopus 로고    scopus 로고
    • Exploring the sequence space of a DNA aptamer using microarrays
    • doi:10.1093/nar/ gkm922
    • Katilius, E., Flores, C. & Woodbury, N. W. 2007 Exploring the sequence space of a DNA aptamer using microarrays. Nucleic Acids Res. 35, 7626-7635. (doi:10.1093/nar/ gkm922)
    • (2007) Nucleic Acids Res , vol.35 , pp. 7626-7635
    • Katilius, E.1    Flores, C.2    Woodbury, N.W.3
  • 13
    • 0023647382 scopus 로고
    • Towards a general theory of adaptive walks on rugged landscapes
    • doi:10.1016/S0022-5193(87)80029-2
    • Kauffman, S. & Levin, S. 1987 Towards a general theory of adaptive walks on rugged landscapes. J. Theoret. Biol. 128, 11-45. (doi:10.1016/S0022-5193(87)80029-2)
    • (1987) J. Theoret. Biol , vol.128 , pp. 11-45
    • Kauffman, S.1    Levin, S.2
  • 14
    • 0024803111 scopus 로고
    • The NK model of rugged fitness landscapes and its application to maturation of the immune response
    • doi:10. 1016/S0022-5193(89)80019- 0
    • Kauffman, S. &Weinberger, E. 1989 The NK model of rugged fitness landscapes and its application to maturation of the immune response. J. Theoret. Biol. 141, 211-245. (doi:10. 1016/S0022-5193(89)80019- 0)
    • (1989) J. Theoret. Biol , vol.141 , pp. 211-245
    • Kauffman, S.1    Weinberger, E.2
  • 15
    • 58549109637 scopus 로고    scopus 로고
    • Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
    • doi:10.1093/nar/gkn899
    • Knight, C. G., Platt, M., Rowe, W., Wedge, D. C., Khan, F., Day, P. J., McShea, A., Knowles, J. & Kell, D. B. 2009 Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape. Nucleic Acids Res. 37, e6. (doi:10.1093/nar/gkn899)
    • (2009) Nucleic Acids Res , vol.37
    • Knight, C.G.1    Platt, M.2    Rowe, W.3    Wedge, D.C.4    Khan, F.5    Day, P.J.6    McShea, A.7    Knowles, J.8    Kell, D.B.9
  • 17
    • 65849401380 scopus 로고    scopus 로고
    • Analysis of aptamer sequence activity relationships
    • doi:10.1039/b814892a
    • Platt, M., Rowe,W., Knowles, J. D., Day, P. J. R. & Kell, D. B. 2009 Analysis of aptamer sequence activity relationships. Integr. Biol. 1, 116-123. (doi:10.1039/b814892a)
    • (2009) Integr. Biol , vol.1 , pp. 116-123
    • Platt, M.1    Rowe, W.2    Knowles, J.D.3    Day, P.J.R.4    Kell, D.B.5
  • 18
    • 33846551980 scopus 로고    scopus 로고
    • Empirical fitness landscapes reveal accessible evolutionary paths
    • doi:10.1038/nature05451
    • Poelwijk, F. J., Kiviet, D. J.,Weinreich, D. M.&Tans, S. J. 2007 Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445, 383-386. (doi:10.1038/nature05451)
    • (2007) Nature , vol.445 , pp. 383-386
    • Poelwijk, F.J.1    Kiviet, D.J.2    Weinreich, D.M.3    Tans, S.J.4
  • 19
    • 0012279561 scopus 로고
    • Epistasis in genetic algorithms: An experimental design perspective
    • Pittsburgh, PA, 15-19 July, San Francisco, CA: Morgan Kaufmann
    • Reeves, C. R. & Wright, C. C. 1995 Epistasis in genetic algorithms: an experimental design perspective. In Proc. 6th Int. Conf. on Genetic Algorithms, Pittsburgh, PA, 15-19 July 1995, pp. 217-224. San Francisco, CA: Morgan Kaufmann.
    • (1995) Proc. 6th Int. Conf. on Genetic Algorithms , pp. 217-224
    • Reeves, C.R.1    Wright, C.C.2
  • 20
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structures
    • doi:10.1098/rspb.1994.0040
    • Schuster, P., Fontana, W., Stadler, P. F. & Hofacker, I. L. 1994 From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B 255, 279-284. (doi:10.1098/rspb.1994.0040)
    • (1994) Proc. R. Soc. Lond. B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 21
    • 34447506391 scopus 로고    scopus 로고
    • Airfoil shape parameterization for optimum Navier-Stokes design with genetic algorithm
    • doi:10. 1016/j.ast.2007.04.004
    • Shahrokhi, A. & Jahangirian, A. 2007 Airfoil shape parameterization for optimum Navier-Stokes design with genetic algorithm. Aerospace Sci. Technol. 11, 443-450. (doi:10. 1016/j.ast.2007.04.004)
    • (2007) Aerospace Sci. Technol , vol.11 , pp. 443-450
    • Shahrokhi, A.1    Jahangirian, A.2
  • 22
    • 0036557854 scopus 로고    scopus 로고
    • Generalized topological spaces in evolutionary theory and combinatorial chemistry
    • doi:10.1021/ci0100898
    • Stadler, B. M. R. & Stadler, P. F. 2002 Generalized topological spaces in evolutionary theory and combinatorial chemistry. J. Chem. Inf. Comput. Sci. 42, 577-585. (doi:10.1021/ci0100898)
    • (2002) J. Chem. Inf. Comput. Sci , vol.42 , pp. 577-585
    • Stadler, B.M.R.1    Stadler, P.F.2
  • 23
    • 0031563773 scopus 로고    scopus 로고
    • Oligonucleotide inhibitors of human thrombin that bind distinct epitopes
    • doi:10.1006/jmbi. 1997.1275
    • Tasset, D. M., Kubik, M. F. & Steiner, W. 1997 Oligonucleotide inhibitors of human thrombin that bind distinct epitopes. J. Mol. Biol. 272, 688-698. (doi:10.1006/jmbi. 1997.1275)
    • (1997) J. Mol. Biol , vol.272 , pp. 688-698
    • Tasset, D.M.1    Kubik, M.F.2    Steiner, W.3
  • 24
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment-RNA ligands to bacteriophage-T4 DNA-polymerase
    • doi:10. 1126/science.2200121
    • Tuerk, C. & Gold, L. 1990 Systematic evolution of ligands by exponential enrichment-RNA ligands to bacteriophage-T4 DNA-polymerase. Science 249, 505-510. (doi:10. 1126/science.2200121)
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 25
    • 0033770580 scopus 로고    scopus 로고
    • Rational evolutionary design: The theory of in vitro protein evolution
    • doi:10.1016/ S0065-3233(01)55003-2
    • Voigt, C. A., Kauffman, S. & Wang, Z. G. 2000 Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem. 55, 79-160. (doi:10.1016/ S0065-3233(01)55003-2)
    • (2000) Adv. Protein Chem , vol.55 , pp. 79-160
    • Voigt, C.A.1    Kauffman, S.2    Wang, Z.G.3
  • 27
    • 0024991769 scopus 로고
    • Correlated and uncorrelated fitness landscapes and how to tell the difference
    • doi:10.1007/BF00202749
    • Weinberger, E. 1990 Correlated and uncorrelated fitness landscapes and how to tell the difference. Biol. Cybernet. 63, 325-336. (doi:10.1007/BF00202749)
    • (1990) Biol. Cybernet , vol.63 , pp. 325-336
    • Weinberger, E.1
  • 28
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: Constraints on the sequence of 'tetraloops'
    • doi:10.1073/pnas.87.21.8467
    • Woese, C. R., Winkers, S. & Gutell, R. R. 1990 Architecture of ribosomal RNA: constraints on the sequence of 'tetraloops'. Proc. Natl Acad. Sci. USA 87, 8467-8471. (doi:10.1073/pnas.87.21.8467)
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winkers, S.2    Gutell, R.R.3
  • 29
    • 0000907353 scopus 로고
    • The roles of mutation, inbreeding, crossbreeding, and selection in evolution
    • Wright, S. 1932 The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proc. 6th Int. Congress on Genetics, pp. 355-366.
    • (1932) Proc. 6th Int. Congress on Genetics , pp. 355-366
    • Wright, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.