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Journal Abstract Search

112 related items for PubMed ID: 15537801

  • 1. Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences.
    Porto M, Roman HE, Vendruscolo M, Bastolla U.
    Mol Biol Evol; 2005 Mar; 22(3):630-8. PubMed ID: 15537801
    [Abstract] [Full Text] [Related]

  • 2. Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.
    Bastolla U, Porto M, Roman HE, Vendruscolo M.
    Gene; 2005 Mar 14; 347(2):219-30. PubMed ID: 15777696
    [Abstract] [Full Text] [Related]

  • 3. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.
    Bastolla U, Porto M, Roman HE, Vendruscolo M.
    BMC Evol Biol; 2006 May 31; 6():43. PubMed ID: 16737532
    [Abstract] [Full Text] [Related]

  • 4. Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.
    Bastolla U, Ortíz AR, Porto M, Teichert F.
    Proteins; 2008 Dec 31; 73(4):872-88. PubMed ID: 18536008
    [Abstract] [Full Text] [Related]

  • 5. Local interactions in protein folding determined through an inverse folding model.
    Bastolla U, Porto M, Ortíz AR.
    Proteins; 2008 Apr 31; 71(1):278-99. PubMed ID: 17932940
    [Abstract] [Full Text] [Related]

  • 6. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues.
    Badasyan A, Liu Z, Chan HS.
    J Mol Biol; 2008 Dec 12; 384(2):512-30. PubMed ID: 18823994
    [Abstract] [Full Text] [Related]

  • 7. Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds.
    Bastolla U, Demetrius L.
    Protein Eng Des Sel; 2005 Sep 12; 18(9):405-15. PubMed ID: 16085657
    [Abstract] [Full Text] [Related]

  • 8. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins.
    Bastolla U, Porto M, Roman HE, Vendruscolo M.
    Proteins; 2005 Jan 01; 58(1):22-30. PubMed ID: 15523667
    [Abstract] [Full Text] [Related]

  • 9. Understanding hierarchical protein evolution from first principles.
    Dokholyan NV, Shakhnovich EI.
    J Mol Biol; 2001 Sep 07; 312(1):289-307. PubMed ID: 11545603
    [Abstract] [Full Text] [Related]

  • 10. Topological thermal instability and length of proteins.
    Burioni R, Cassi D, Cecconi F, Vulpiani A.
    Proteins; 2004 May 15; 55(3):529-35. PubMed ID: 15103617
    [Abstract] [Full Text] [Related]

  • 11. Design of amino acid sequences to fold into C(alpha)-model proteins.
    Amatori A, Tiana G, Sutto L, Ferkinghoff-Borg J, Trovato A, Broglia RA.
    J Chem Phys; 2005 Aug 01; 123(5):054904. PubMed ID: 16108690
    [Abstract] [Full Text] [Related]

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  • 13. Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.
    Li H, Tang C, Wingreen NS.
    Proteins; 2002 Nov 15; 49(3):403-12. PubMed ID: 12360530
    [Abstract] [Full Text] [Related]

  • 14. Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins.
    Morra G, Colombo G.
    Proteins; 2008 Aug 15; 72(2):660-72. PubMed ID: 18247351
    [Abstract] [Full Text] [Related]

  • 15. A statistical model for predicting protein folding rates from amino acid sequence with structural class information.
    Gromiha MM.
    J Chem Inf Model; 2005 Aug 15; 45(2):494-501. PubMed ID: 15807515
    [Abstract] [Full Text] [Related]

  • 16. Understanding the role of the topology in protein folding by computational inverse folding experiments.
    Mucherino A, Costantini S, di Serafino D, D'Apuzzo M, Facchiano A, Colonna G.
    Comput Biol Chem; 2008 Aug 15; 32(4):233-9. PubMed ID: 18479970
    [Abstract] [Full Text] [Related]

  • 17. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.
    Mayrose I, Graur D, Ben-Tal N, Pupko T.
    Mol Biol Evol; 2004 Sep 15; 21(9):1781-91. PubMed ID: 15201400
    [Abstract] [Full Text] [Related]

  • 18. Physical origins of protein superfamilies.
    Zeldovich KB, Berezovsky IN, Shakhnovich EI.
    J Mol Biol; 2006 Apr 07; 357(4):1335-43. PubMed ID: 16483605
    [Abstract] [Full Text] [Related]

  • 19. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes.
    Parisi G, Echave J.
    Gene; 2005 Jan 17; 345(1):45-53. PubMed ID: 15716088
    [Abstract] [Full Text] [Related]

  • 20. Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments.
    Godoy-Ruiz R, Ariza F, Rodriguez-Larrea D, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM.
    J Mol Biol; 2006 Oct 06; 362(5):966-78. PubMed ID: 16935299
    [Abstract] [Full Text] [Related]

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