List of Publications

  1. Antonio F. Pereira de Araujo

    2. Increasing discrepancy between absolute and effective indexes of research output in a Brazilian academic department.
    Scientometrics, 2008, 77, 425-437. reprint (pdf) ,
     
  2. Antonio F. Pereira de Araujo, Antonio L. C. Gomes, Alexandre A. Bursztyn and Eugene I. Shakhnovich.

    3. Native atomic burials, supplemented by physically motivated hydrogen bond constrains, contain sufficient information to determine the tertiary structure of small globular proteins
    Proteins:Structure, Function and Bioinformatics, 2008, 70, 971-983. reprint (pdf) ,
     
  3. Gustavo M. N. Fleury, Marco A. A. Barbosa and Antonio F. Pereira de Araujo

    4. Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models.
    Physical Review E, 2007, 76, 051914. reprint (pdf) ,
     
  4. Antonio L. C. Gomes, Julia R. de Rezende, Antonio F. Pereira de Araujo and Eugene I. Shakhnovich.

    5. Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions.
    Proteins:Structure, Function and Bioinformatics, 2007, 66, 304-320. reprint (pdf) ,
     
  5. Leandro G. Garcia and Antonio F. Pereira de Araujo.

    6. Folding pathway dependence on energetic frustration and interaction heterogeneity for a three dimensdional hydrophobic protein model.
    Proteins:Structure, Function and Bioinformatics, 2006, 62, 46-63. reprint (pdf) ,
     
  6. Antonio F. Pereira de Araujo.

    7. Protein folding cooperativity: Basic insights from minimalist models.
    Protein and Peptide Letters, 2005, 12, 223-228. preprint (pdf) ,
     
  7. Marco A. A. Barbosa, Leandro G. Garcia and Antonio F. Pereira de Araujo.

    8. Entropy reduction effect imposed by hydrogen bond formation on protein folding cooperativity: Evidence from a hydrophobic minimalist model.
    Physical Review E, 2005, 72, ID 051903 . reprint (pdf) ,
     
  8. Marco A. A. Barbosa and Antonio F. Pereira de Araujo.

    9. Effect of structural segregation and chain compaction on the thermodynamics of folding of a hydrophobic protein model.
    Physical Review E, 2003, 67, ID 051919. reprint (pdf) ,
     
  9. Werner L. Treptow, Marco Aurelio A. Barbosa, Leandro G. Garcia and Antonio F. Pereira de Araujo.

    10. Non-native interactions, effective contact order and proten folding: A mutational investigation with the energetically frustrated hydrophobic model.
    Proteins: Structure, Function and Genetics, 2002, 49, 167-180.
    preprint (html) ,  reprint (pdf) ,
     
  10. Leandro Guimaraes Garcia, Werner L. Treptow and Antonio F. Pereira de Araujo.

    11. Folding simulations of a three-dimesional protein model with an non-specific hydrophobic energy function.
    Physical Review E, july 2001.
    preprint (html) ,  reprint (pdf) ,
     
  11. Antonio F. Pereira de Araujo.

    12. Sequence rotation in N-dimensional space and the folding of hydrophobic protein models. Surpassing the diagonal unfolded state approximation.
    Journal of Chemical Physics, 2001, 114(1), 570-578.
    preprint (html) ,  reprint (pdf) ,
     
  12. Antonio F. Pereira de Araujo.

    13. Folding protein models with a simple hydrophobic energy function. The fundamental importance of monomer inside/outside segregation.
    PNAS, 1999, 96(22):12482-12487.
    reprint (pdf) ,  preprint (html) ,  preprint (postscript)
     
  13. Antonio F. Pereira de Araujo, Thomas C. Pochapsky and Brian Joughin.

    14. Thermodynamics of interactions between amino acid side chains: Experimental differentiation of aromatic-aromatic, aromatic-aliphatic and aliphatic-aliphatic side chain interactions in water.
    Biophysical Journal 76 (5) 2319-2328, 1999.
    reprint (pdf)
     
  14. Antonio F. Pereira de Araujo and Thomas C. Pochapsky.

    15. Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition experiments.
    Folding&Design 2 (2):135-139, 1997.
    preprint (html) ,  reprint (pdf)
     
  15. Antonio F. Pereira de Araujo and Thomas C. Pochapsky.

    16. Monte Carlo simulations of protein folding using inexact potentials. How accurate must parameters be in order to preserve the essential features of the energy landscape?
    Folding&Design 1 (4):299-314, 1996.
    preprint (html) ,  reprint (pdf)
    obs: Este artigo foi citado como "of special interest" por A. Finkelstein em Curr. Opin. in Struct. Biol., 2/97.
     
  16. Antonio F. Pereira de Araujo - Ph.D. Thesis.

    17. Prof. Thomas C. Pochapsky (advisor).
    Requirements for protein folding potentials: perspectives from lattice model simulations.
    Graduate Program in Biophysics, Brandeis University, Waltham MA, USA.
    February 1998 (defended and approved: May 1997).
     html  ,  postscript
     
  17. Antonio F. Pereira de Araujo - Tese de Mestrado.

    18. Prof. Manuel M. Ventura (orientador).
    Predicao de estrutura secundaria de proteinas globulares: implementacao dos principais algoritmos reunidos no pacote COMBINE e sua utilizacao na analise da regiao C-terminal da PABP.
    Pos-graduacao em Biologia Molecular, UnB, Brasilia DF, Brasil, 1992.