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Articles on protein folding and evolution

  1. Jímenez-Santos MJ, Arenas M, Bastolla U.
    Substitution rates support stability-constrained versus structurally-constrained models of protein evolution.
    Mol Biol Evol, submitted (2017).

  2. de la Higuera I, Ferrer-Orta C, de Ávila AI, Perales C, Sierra M, Singh K, Sarafianos SG, Dehouck Y, Bastolla U, Verdaguer N, Domingo E.
    Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.
    Genome Biol Evol. 2017 May 1;9(5):1212-1228. [Pubmed]

  3. Bastolla U, Dehouck Y, Echave J.
    What evolution tells us about protein physics, and protein physics tells us about evolution.
    Curr Opin Struct Biol. 2017 Feb;42:59-66. [Pubmed]

  4. Arenas M, Weber CC, Liberles DA, Bastolla U.
    ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Syst Biol. 2017 66:1054-1064. [Pubmed]

  5. Nido GS, Bachschmid-Romano L, Bastolla U, Pascual-García A.
    Learning structural bioinformatics and evolution with a snake puzzle.
    PeerJ Computer Science 2016. 2:e100 [PeerJ]

  6. Arenas M, Sánchez-Cobos A, Bastolla U.
    Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.
    Mol Biol Evol. 2015 32:2195-207. [Pubmed]

  7. Bastolla U.
    Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution.
    Biomolecules. 2014 Mar 7;4(1):291-314. doi: 10.3390/biom4010291. [Pubmed]

  8. Minning J, Porto M, Bastolla U.
    Detecting selection for negative design in proteins through an improved model of the misfolded state.
    Proteins. 2013 Jul;81(7):1102-12. doi: 10.1002/prot.24244. [Pubmed]

  9. M Arenas, HG Dos Santos, D Posada, U Bastolla
    Protein evolution along phylogenetic histories under structurally constrained substitution models.
    Bioinformatics, 530 4 2013 [Pubmed]

  10. U. Bastolla, M. Porto.
    Modeling structural and genomic constraints in the evolution of proteins.
    In: Computational Modeling of Biological Systems: From Molecules to Pathways. Ed: Nikolay Dokholyan. Springer Verlag (New York - Heidelberg), 2002. [Book]

  11. Bastolla U, Bruscolini P, Velasco JL.
    Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding.
    Proteins. 2012 Aug;80(9):2287-304. doi: 10.1002/prot.24118. Epub 2012 Jun 18. [Pubmed]

  12. Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.
    The interface of protein structure, protein biophysics, and molecular evolution.
    Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. [Pubmed]

  13. R. Méndez; M. Fritsche; M. Porto and U.Bastolla
    Mutation bias favors protein folding stability in the evolution of small populations.
    PLoS Comput Biol 6(5): e1000767 2010. [Pubmed]

  14. S. Sammet; U. Bastolla and M. Porto
    Comparison of translation loads for standard and alternative genetic codes.
    BMC Evol. Biol. 2010, 10:178 [Pubmed]

  15. F. Teichert; J.Minning; U. Bastolla and M. Porto
    High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH.
    BMC Bioinformatics 2010, 11:251 [Pubmed]

  16. U.Bastolla, M.Porto, E.H. Roman, M.Vendruscolo (Eds.)
    Structural approaches to sequence evolution: Molecules, networks, population.
    Springer-Verlag (Berlin), 2008. [Book]

  17. U.Bastolla, M.Porto, E.H. Roman, M.Vendruscolo.
    The structurally constrained neutral model of protein evolution.
    In: Structural approaches to sequence evolution: Molecules, networks, population. Eds: U.Bastolla, M.Porto, E.H. Roman, M.Vendruscolo. Springer-Verlag, Berlin (2008). [Book]

  18. Bastolla, U.; Ortiz A.R.; Porto, M.; Teichert, F.
    Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences.
    Proteins 2008, 73: 872-888. [Pubmed] [PDF]

  19. Bastolla, U.; Porto, M.; Ortiz, A.R.
    Local interactions in protein folding determined through an inverse folding model.
    Proteins 2008, 71:278-99 [Pubmed] [PDF]

  20. Han, R.; Leo-Macias, A.; Zerbino, D.; Bastolla U.; Contreras-Moreira, B.; Ortiz, A.R.
    An efficient conformational sampling method for Homology Modeling.
    Proteins 2008, 71: 175-178 [Pubmed] [PDF]

  21. 2007

  22. Teichert, F.; Bastolla, U.; Porto, M.
    SABERTOOTH: protein structural alignment based on a vectorial structure representation.
    BMCBioinformatics 2007, 8: 425 [Pubmed] [PDF]

  23. Bastolla, U; Porto, M.; Romn, H.E.
    A protein evolution model with independent sites that reproduces site-specific amino acid distribuitons from the Protein Data Bank.
    BMC Evol. Biol. (2006). [Pubmed] [PDF]

  24. Bastolla, U.; Demetrius, L.
    Stability contraints and protein evolution: the role of chain lenght, composition and disulfide bonds.
    Protein Eng. Des, Sel. 18(9): 405-15. [Pubmed] [PDF]

  25. M.Porto, E.H.Roman, M.Vendruscolo, U.Bastolla.
    Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences.
    Mol.Biol..Evol. 22: 630-638 (2005) [Article]

  26. C. Briones, U.Bastolla.
    Protein evolution in viral quasispecies under selective pressure: a thermodynamic and phylogenetic analysis.
    Gene, 347/2: 237-246 (2005) [Article]

  27. U.Bastolla, M.Porto, E.H. Roman, M.Vendruscolo.
    Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.
    Gene, 347/2: 219-230 (2005) [Article]

  28. U. Bastolla.
    Plegamiento de proteínas: un puente entre la biología y la física.
    Revista de la Real Sociedad Española de Física 19, 3:17-23 (2005)

  29. U.Bastolla, M.Porto, E.H.Roman, M.Vendruscolo.
    Principal eigenvector of contact matrices and hydrophobicity profiles in proteins.
    Proteins, 58: 22-30 (2005) [Article]

  30. E.Huedo, U.Bastolla, R.Montero, I.M.Llorente.
    A framework for protein structure prediction on the grid
    New Generation Computing 23, 277-290 (2005) [Article]

  31. U.Bastolla, A.Moya, E.Viguera, R.C.H.J. van Ham.
    Genomic determinants of protein folding thermodynamics in prokaryotic organisms.
    J.Mol.Biol. 343: 1451-66 (2004) [Article]

  32. M.Porto, U.Bastolla, E.H.Roman, M.Vendruscolo.
    Reconstruction of protein structures from a vectorial representation.
    Phys. Rev. Lett. 92: 218101 (2004) [Article]

  33. E.Huedo, U.Bastolla, R.Montero, I.M.Llorente.
    Computational proteomics on the grid.
    New Gen. Comp. 22, 191-192 (2004) [Article]

  34. R. van Ham, J. Kamerbeek, C. Palacios, C. Rausell, F. Abascal, U. Bastolla, J.M. Fernandez, L. Jimenez, M. Postigo, F.J. Silva, J. Tamames, E. Viguera, A. Latorre, A. Valencia, F. Moran, A. Moya.
    Reductive genome evolution in Buchnera aphidicola.
    Proc. Natl. Acad. Sci. USA. 100: 581-586 (2003) [Article]

  35. U.Bastolla, M. Porto, E.H. Roman, M.Vendruscolo.
    Statistical properties of neutral evolution.
    J. Mol. Evol. 57, S103-S119 (2003) [Article]

  36. U.Bastolla, M. Porto, E.H. Roman, M.Vendruscolo.
    Connectivity of neutral networks and structural conservation in protein evolution.
    J. Mol. Evol. 56: 243-254 (2003) [Article]

  37. U.Bastolla, M. Porto, E.H. Roman, M.Vendruscolo.
    Lack of self-averaging in neutral evolution of proteins.
    Phys. Rev. Lett.. 89: 208101 (2002) [Article]

  38. S. Wallin, J. Farwer, U. Bastolla.
    Testing distance measures with continuous and discrete protein models.
    Proteins 50 144-157 (2002) [Article]

  39. U.Bastolla, M. Vendruscolo.
    Correlated energy landscapes and protein evolution.
    In: Recent Developments in Protein Folding, Stability and Design, Research Signpost , 2002 [Article]

  40. U.Bastolla, Farwer J., E.W. Knapp, M.Vendruscolo.
    How to guarantee optimal stability to most representative structures in the Protein Data Bank.
    Proteins 44,79-96 (2001) [Article]

  41. U. Bastolla, P. Grassberger.
    Exactness of the annealed and of the replica symmetric approximation for random heteropolymers
    Phys. Rev. E 63 1901-1913 (2001) [Article]

  42. U. Bastolla
    Overlap distribution in random and designed heteropolymers.
    Eur. Phys. J. E 4, 305-313 (2001) [Article]

  43. U.Bastolla, M.Vendrsucolo, E.W. Knapp.
    A statistical mechanical method to optimize energy parameters for protein folding.
    Procl. Natl. Acad. Sci. USA 97, 3977-3981 (2000) [Article]

  44. U.Bastolla, M.Vendrsucolo, E.H. Roman
    Structurally constrained protein evolution: results from a lattice simulation.
    Eur. Phys. J. B. 15, 385-397 (2000) [Article]

  45. U.Bastolla, H.Frauenkron, P.Grassberger.
    Phase Diagram of random heteropolymers: replica approach and application of a new Monte Carlo algorithm.
    J. Mol. Liq. 84, 111-129 (2000) [Article]

  46. U.Bastolla, M.Vendruscolo, E.H. Roman.
    Neutral evolution of model proteins: diffusion in sequence space and overdispersion.
    J. Theor. Biol. 200, 49-64 (1999) [Article]

  47. [Article]

  48. G.T. Barkema, U. Bastolla & P. Grassberger.
    Two-dimensional oriented self-avoiding walks with parallel contacts.
    J. Stat. Phys., 90, 1311-1324 (1998) [Article]

  49. H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, W. Nadler.
    New Monte Carlo algorithm for protein folding.
    Phys. Rev. Lett. 80, 3149-3152 (1998) [Article]

  50. U. Bastolla, H. Frauenkron, E. Gerstner, P. Grassberger, W. Nadler.
    Testing a new Monte Carlo algorithm for protein folding.
    Proteins 32: 52-66(1998) [Article]

  51. U. Bastolla, P. Grassberger.
    Phase transitions of single semi-stiff polymer chains.
    J. Stat. Phys. 89, 1061-1078 (1997) [Article]

  52. L.Peliti, U.Bastolla.
    Collective adaptation in a statistical model of an evolving population.
    C.R. Acad. Sci. Paris, 317:371-371 (1994) [Article]

  53. U.Bastolla, L.Peliti.
    Un modele statistique d’évolution avec selection stabilisante.
    C.R. Acad. Sci. Paris, 313, Serie III, 101-105 (1991)

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