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A topological measurement of protein compressibility (2015)

  • Authors:
  • USP affiliated authors: GAMEIRO, MÁRCIO FUZETO - ICMC
  • USP Schools: ICMC
  • DOI: 10.1007/s13160-014-0153-5
  • Subjects: TOPOLOGIA; EQUAÇÕES DIFERENCIAIS; EQUAÇÕES DIFERENCIAIS ORDINÁRIAS
  • Keywords: Protein compressibility; Computational topology; Persistence diagram
  • Language: Inglês
  • Imprenta:
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    Informações sobre o DOI: 10.1007/s13160-014-0153-5 (Fonte: oaDOI API)
    • Este periódico é de assinatura
    • Este artigo NÃO é de acesso aberto
    • Cor do Acesso Aberto: closed
    Versões disponíveis em Acesso Aberto do: 10.1007/s13160-014-0153-5 (Fonte: Unpaywall API)

    Título do periódico: Japan Journal of Industrial and Applied Mathematics

    ISSN: 0916-7005,1868-937X



      Não possui versão em Acesso aberto
    Informações sobre o Citescore
  • Título: Japan Journal of Industrial and Applied Mathematics

    ISSN: 0916-7005

    Citescore - 2017: 0.62

    SJR - 2017: 0.472

    SNIP - 2017: 0.611


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    • ABNT

      GAMEIRO, Márcio Fuzeto; HIRAOKA, Yasuaki; IZUMI, Shunsuke; et al. A topological measurement of protein compressibility. Japan journal of industrial and applied mathematics, Tokyo, Japan, Springer, v. 32, n. 1, p. 1-17, 2015. Disponível em: < http://dx.doi.org/10.1016/j.physd.2015.11.011 > DOI: 10.1007/s13160-014-0153-5.
    • APA

      Gameiro, M. F., Hiraoka, Y., Izumi, S., Kramar, M., Mischaikow, K., & Nanda, V. (2015). A topological measurement of protein compressibility. Japan journal of industrial and applied mathematics, 32( 1), 1-17. doi:10.1007/s13160-014-0153-5
    • NLM

      Gameiro MF, Hiraoka Y, Izumi S, Kramar M, Mischaikow K, Nanda V. A topological measurement of protein compressibility [Internet]. Japan journal of industrial and applied mathematics. 2015 ; 32( 1): 1-17.Available from: http://dx.doi.org/10.1016/j.physd.2015.11.011
    • Vancouver

      Gameiro MF, Hiraoka Y, Izumi S, Kramar M, Mischaikow K, Nanda V. A topological measurement of protein compressibility [Internet]. Japan journal of industrial and applied mathematics. 2015 ; 32( 1): 1-17.Available from: http://dx.doi.org/10.1016/j.physd.2015.11.011

    Referências citadas na obra
    Balog, E., Perahia, D., Smith, J., Merzel, F.: Vibrational softening of a protein on ligand binding. J. Phys. Chem. B 115(21), 6811–6817 (2011)
    Borsuk, K.: On the imbedding of systems of compacta in simplicial complexes. Fund. Math. 35, 217–234 (1948)
    Carlsson, G.: Topology and data. Bull. Am. Math. Soc. 46(2), 255–308 (2009)
    Chazal, F., Cohen-Steiner, D., Glisse, M., Guibas, L., Oudot S. : Proximity of persistence modules and their diagrams. In: Proceedings of the Twenty-fifth Annual Symposium on Computational Geometry, pp. 237–246 (2009)
    Cohen-Steiner, D., Edelsbrunner, H., Harer, J.: Stability of persistence diagrams. Discrete Comput. Geom. 37, 103–120 (2007)
    Dey, T., Hirani, A., Krishnamoorthy B.: Optimal homologous cycles, total unimodularity and linear programming. SIAM J. Comput. 40, 1026–1044 (2011)
    Dumas, J.-G., Heckenbach, F., Saunders, B.D., Welker, V.: Computing simplicial homology based on efficient Smith normal form algorithms. Algebra, Geometry and Software Systems, pp. 177–206 (2003)
    Edelsbrunner, H.: The union of balls and Its dual shape. Discrete Comput. Geom. 13, 415–440 (1995)
    Edelsbrunner, H., Harer, J.: Persistent homology—a survey. In: Surveys on Discrete and Computational Geometry, vol. 453, pp. 257–282. American Mathematical Society, Providence (2008)
    Gekko, K., Araga, M., Kamiyama, T., Ohmae, E., Akasaka, K.: Nonneutral evolution of volume fluctuations in lysozymes revealed by normal-mode analysis of compressibility. Biophys. Chem. 144(1–2), 67–71 (2009)
    Gekko, K., Hasegawa, Y.: Compressibility-structure relationship of globular proteins. Biochemistry 25, 6563–6571 (1986)
    Gekko, K., Noguchi, H.: Compressibility of globular proteins in water at $$25\,^{\circ }$$ 25 ∘ C. J. Phys. Chem. 83(21), 2706–2714 (1979)
    Gekko, K., Tamura, Y., Ohmae, E., Hayashi, H., Kagamiyama, H., Ueno, H.: A large compressibility change of protein induced by a single amino acid substitution. Protein Sci. 5(3), 542–545 (1996)
    Gromiha, M., Ponnuswamy, P.K.: Relationship between amino acid properties and protein compressibility. J. Theor. Biol. 165, 87–100 (1993)
    Harker, S., Mischaikow, K., Mrozek, M., Nanda, V.: Discrete Morse theoretic algorithms for computing homology of complexes and maps. Found. Comput. Math. (2012). doi: 10.1007/s10208-013-9145-0
    Hatcher, A.: Algebraic Topology. Cambridge University Press (2002)
    Kharakoz, D.: Protein compressibility, dynamics, and pressure. Biophys. J. 79, 511–525 (2000)
    Leu, B., Alatas, A., Sinn, H., Alp, E., Said, A., Yavaş, H., Zhao, J., Sage, J., Sturhahn, W.: Protein elasticity probed with two synchrotron-based techniques. J. Chem. Phys. 132, 085103 (2010)
    Liang, J., Edelsbrunner, H., Fu, P., Sudharkar, P.V., Subramaniam, S.: Analytic shape computation of macromolecules I: molecular area and volume through alpha shape. Proteins Struct. Funct. Genet. 33, 1–17 (1998)
    Sanchez-Ruiz, J.M.: Protein kinetic stability. Biophys. Chem. 148(1–3), 1–15 (2010)
    Sheffler, W., Baker, D.: RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci. 18, 229–239 (2009)
    Tahbaz-Salehi, A., Jadbabaie, A.: Distributed coverage verification in sensor networks without location information. IEEE Trans. Auto. Control 55, 1837–1849 (2010)
    Yamamoto, T., Izumi, S., Gekko, K.: Mass spectrometry on hydrogen/deuterium exchange of dihydrofolate reductase: effects of ligand binding. J. Biochem. 135(6), 663–671 (2004)
    Uversky, V.: Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11(4), 739–756 (2002)
    Zaccai, G.: How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288, 1604 (2000)
    Zomorodian, A., Carlsson, G.: Computing persistent homology. Discrete Comput. Geom. 33, 249–274 (2005)
    CGAL webpage. http://www.cgal.org/
    CHomP webpage. http://chomp.rutgers.edu/
    Naccess. http://www.bioinf.manchester.ac.uk/naccess/
    Perseus webpage. http://www.math.rutgers.edu/~vidit/perseus.html
    PDB. http://www.rcsb.org/