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Preprint


  1. Pascual-García A, Arenas M, Bastolla U.
    The molecular clock in the evolution of protein structures.
    Mol Biol Evol, submitted (2017).


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

Publicados

    2017

  1. Dehouck Y, Bastolla U.
    The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network models.
    Integr Biol (Camb). 2017 Jul 17;9(7):627-641. [Pubmed]

  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. Pascual-García A, Bastolla U.
    Mutualism supports biodiversity when the direct competition is weak.
    Nat Commun. 2017 Feb 24;8:14326. [Pubmed]

  4. A Ferrera, A Pascual-García, U Bastolla.
    Effective competition determines the global stability of model ecosystems .
    Theor Ecol. 2017, 10: 195–205. [article]

  5. Pascual-García A, Bastolla U.
    The architecture of mutualistic networks does influence structural stability.
    Self-Journal of Science (2017). [article]

  6. Berezovsky IN, Bastolla U.
    Editorial overview: Proteins: bridging theory and experiment.
    Curr Opin Struct Biol. 2017 Feb;42:viii-x. [Pubmed]

  7. 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]

  8. 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]

  9. 2016

  10. 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]

  11. 2015

  12. 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]

  13. 2014

  14. Pascual-García A, Tamames J, Bastolla U.
    Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?
    BMC Microbiol. 2014 14:284. [Pubmed]

  15. Bruix M, Treviño MA, García-Mayoral MF, Jiménez MÁ, Bastolla U.
    Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins.
    Biochim Biophys Acta. 2014 Oct;1844(10):1808-19. doi: 10.1016/j.bbapap.2014.07.019. Epub 2014 Aug 1. [Pubmed]

  16. Bastolla U.
    Computing protein dynamics from protein structure with elastic network models
    Wiley Interdisciplinary Reviews: Computational Molecular Science. 04/2014; [Pubmed]

  17. 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]

  18. Sequeira-Mendes J, Aragüez I, Peiró R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C.
    The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States.
    Plant Cell. 2014 Jun 16;26(6):2351-2366. [Epub ahead of print]

  19. M Benguigui, M Arenas
    Spatial and Temporal Simulation of Human Evolution. Methods, Frameworks and Applications.
    Current genomics 15 (4), 245-255 2014 [Pubmed]

  20. M Arenas, D Posada
    Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories.
    Molecular biology and evolution, msu078 1 2014 [Pubmed]

  21. M Arenas, S Mona, A Trochet, AS HANULOVA, M Currat, N Ray, L Chikhi, ...
    The scaling of genetic diversity in a changing and fragmented world.
    Scaling in Ecology and Biodiversity Conservation. Pensoft Publishers, Sofia ... 2 2014 [Pubmed]

  22. Borroto A, Abia D, Alarcón B.
    Crammed signaling motifs in the T-cell receptor.
    Immunol Lett. 2014 Sep;161(1):113-7. doi: 10.1016/j.imlet.2014.05.007. Epub 2014 May 27. [Pubmed]

  23. Vallés Y, Gosalbes MJ, Ferrús ML, Artacho A, Pascual-García A, Abellán JJ and Francino, MP.
    Successional Patterns of Community Assembly and Functional Ecology During Gut Microbiota Development.
    PLoS Genet 2014. 10(6): e1004406 [Pubmed]

  24. 2013

  25. 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]

  26. Bastolla U, Porto M, Roman HE.
    The emerging dynamic view of proteins: protein plasticity in allostery, evolution and self-assembly.
    Biochim Biophys Acta. 2013 May;1834(5):817-9. doi: 10.1016/j.bbapap.2013.03.016. [Pubmed]

  27. Dos Santos HG, Klett J, Méndez R, Bastolla U.
    Characterizing conformation changes in proteins through the torsional elastic response.
    Biochim Biophys Acta. 2013 May;1834(5):836-46. doi: 10.1016/j.bbapap.2013.02.010. Epub 2013 Feb 19. [Pubmed]

  28. M Arenas, HG Dos Santos, D Posada, U Bastolla
    Protein evolution along phylogenetic histories under structurally constrained substitution models.
    Bioinformatics, btt530 4 2013 [Pubmed]

  29. Dos Santos HG, Abia D, Janowski R, Mortuza G, Bertero MG, Boutin M, Guarín N, Méndez-Giráldez R, Nuñez A, Pedrero JG, Redondo P, Sanz M, Speroni S, Teichert F, Bruix M, Carazo JM, González C, Reina J, Valpuesta JM, Vernos I, Zabala JC, Montoya G, Coll M, Bastolla U, Serrano L
    Structure and Non-Structure of Centrosomal Proteins.
    PloS one 8 (5), e62633 [Pubmed]

  30. Lombraña R, Almeida R, Revuelta I, Madeira S, Herranz G, Saiz N, Bastolla U, Gómez M.
    High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins.
    EMBO J. 2013 32:2631-44. [Pubmed]

  31. Matamoros T, Barrioluengo V, Abia D, Menéndez-Arias L.
    Major groove binding track residues of the connection subdomain of human immunodeficiency virus type 1 reverse transcriptase enhance cDNA synthesis at high temperatures.
    Biochemistry. 2013 52:9318-28. doi: 10.1021/bi401390x. Epub 2013 Dec 12. [Pubmed]

  32. Singh PK, Ramachandran G, Ramos-Ruiz R, Peiró-Pastor R, Abia D, Wu LJ, Meijer WJ.
    Mobility of the native Bacillus subtilis conjugative plasmid pLS20 is regulated by intercellular signaling.
    PLoS Genet. 2013 Oct;9(10):e1003892. doi: 10.1371/journal.pgen.1003892. Epub 2013 Oct 31. [Pubmed]

  33. S Mona, N Ray, M Arenas, L Excoffier
    Genetic consequences of habitat fragmentation during a range expansion.
    Heredity 3 2013 [Pubmed]

  34. JS Lopes, M Arenas, D Posada, MA Beaumont
    Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.
    Heredity 112 (3), 255-264 3 2013 [Pubmed]

  35. M Arenas
    The importance and application of the ancestral recombination graph.
    Frontiers in genetics 4 [Pubmed]

  36. Alvarez-Navarro C, Cragnolini JJ, Dos Santos HG, Barnea E, Admon A, Morreale A, López de Castro JA.
    Novel HLA-B27-restricted epitopes from Chlamydia trachomatis generated upon endogenous processing of bacterial proteins suggest a role of molecular mimicry in reactive arthritis.
    Biol Chem. 2013 Jul 18. [Pubmed]

  37. Miguel Arenas
    Computer programs and methodologies for the simulation of DNA sequence data with recombination.
    Front Genet. 4:9 (2013) [Pubmed]

  38. 2012

  39. 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]

  40. 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]

  41. Elena Lorente, Susana Infantes, David Abia, Eilon Barnea, Ilan Beer, Ruth García, Fátima Lasala, Mercedes Jiménez, Carmen Mir, Antonio Morreale, Arie Admon, Daniel López
    A Viral, Transporter Associated with Antigen Processing (TAP)-independent, High Affinity Ligand with Alternative Interactions Endogenously Presented by the Nonclassical Human Leukocyte Antigen E Class I Molecule.
    Journal of Biological Chemistry 287 (42), 34895-34903 [Pubmed]

  42. Lorena Gallego-Villar, Celia Pérez-Cerdá, Belén Pérez, David Abia, Magdalena Ugarte, Eva Richard, Lourdes R Desviat
    Functional characterization of novel genotypes and cellular oxidative stress studies in propionic acidemia.
    Journal of inherited metabolic disease, 1-10 [Pubmed]

  43. Javier Klett, Alfonso Núñez-Salgado, Helena G. Dos Santos, Álvaro Cortés-Cabrera, Almudena Perona, Rubén Gil-Redondo, David Abia, Federico Gago, and Antonio Morreale
    MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking.
    J. Chem. Theory Comput., 8, 3395-3408 (2012) [Pubmed]

  44. Álvaro Cortés Cabrera, Javier Klett, Helena G. Dos Santos, Almudena Perona, Rubén Gil-Redondo, Sandrea M. Francis, Eva M. Priego, Federico Gago, and Antonio Morreale
    CRDOCK: An Ultrafast Multipurpose Protein−Ligand Docking Tool.
    J. Chem. Inf. Model., 52, 2300-20309 (2012)[Pubmed]

  45. Claire Coderch, Javier Klett, Antonio Morreale, J. Fernando Díaz, and Federico Gago
    Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β-Tubulin.
    Chem. Med. Chem., 7, 836 – 843, 2012 [Pubmed]

  46. Antonio Morreale and Federico Gago
    COMparative BINding Energy (COMBINE) Analysis as a Structure-Based 3D-QSAR Method.
    Physico-Chemical and Computational Approaches to Drug Discovery. RSC Drug Discovery Series, 23, 244-272 (2012) [Pubmed]

  47. Romero O, Filice M, Rivas Bde L, Carrasco-Lopez C, Klett J, Morreale A, Hermoso JA, Guisan JM, Abian O, Palomo JM.
    Semisynthetic peptide-lipase conjugates for improved biotransformations.
    Chem Commun (Camb). 2012 Sep 18;48(72):9053-5. Epub 2012 [Pubmed]

  48. Álvaro Cortés-Cabrera, Federico Gago, and Antonio Morreale
    A reverse combination of structure-based and ligand-based strategies for virtual screening.
    J. Comput.-Aided Mol. Des., 26, 319–327, 2012 [Pubmed]

  49. Juan Bueren-Calabuig; Ana Negri; Federico; Antonio Morreale; and Federico Gago
    Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity.
    Organic& Biomolecular Chemistry, accepted (2011) [Pubmed]

  50. 2011

  51. G. S. Nido; R. Méndez; A. Pascual-García; D. Abia and U. Bastolla
    Protein disorder in the centrosome correlates with complexity in cell types number.
    Mol. BioSyst., 2012, DOI: 10.1039/c1mb05199g [Pubmed]

  52. Gonzalo Pérez-Siles; Enrique Núñez; Antonio Morreale; Esperanza Jiménez; Alejandra Leo-Macías; Guillermo Pita; Francesca Cherubino; Rachele Sangaletti; Elena Bossi; Ángel R. Ortíz; Carmen Aragón and Beatriz López-Corcuera
    An aspartate residue in the external vestibule of glycine transporter 2 (GLYT2) controls cation access and transport coupling.
    Biochemical Journal [Pubmed]

  53. Claire Coderch; Antonio Morreale; and Federico Gago
    Tubulin-based structure-affinity relationships for antimitotic Vinca alkaloids
    Anti-cancer agents in medicinal chemistry, in the press (2011) [Pubmed]

  54. Bermudo R; Abia D; Mozos A; García-Cruz E; Alcaraz A; Ortiz AR; Thomson TM; Fernández PL.
    Highly sensitive molecular diagnosis of prostate cancer using surplus material washed off from biopsy needles.
    Br J Cancer. 2011 Nov 8;105(10):1600-7. doi: 10.1038/bjc.2011.435. Epub 2011 Oct 18. [Pubmed]

  55. Álvaro Cortés-Cabrera; Rubén Gil-Redondo; Almudena Perona A; Federico Gago; and Antonio Morreale
    VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface
    J. Comput.-Aided Mol. Design, 25, 813-824 (2011) [Pubmed]

  56. Gonzalo Pérez-Siles; Antonio Morreale; Alejandra Leo-Macías; Guillermo Pita; Ángel R. Ortíz; Carmen Aragón; Beatriz López-Corcuera
    Molecular basis of the differential interaction with lithium of glycinetransporters GLYT1 and GLYT2
    J. Neurochem., 118, 195-204 (2011) [Pubmed]

  57. Emna Maalej; Fakher Chabchoub; Abdelouahid Samadi; Cristóbal de los Ríos; Almudena Perona; Antonio Morreale; José Marco-Contelles
    Synthesis, biological assessment and molecular modeling of 14-aryl-10,11,12,14-tetrahydro-9H-benzo[5,6]chromeno[2,3-b]quinolin-13-amines
    Bioorg. Med. Chem. Lett., 21, 2384-2388 (2011) [Pubmed]

  58. Vega AI; Pérez-Cerdá C; Abia D; Gámez A; Briones P; Artuch R; Desviat LR; Ugarte M; Pérez B.
    Expression analysis revealing destabilizing mutations in phosphomannomutase 2 deficiency (PMM2-CDG): expression analysis of PMM2-CDG mutations.
    J Inherit Metab Dis. 2011 Aug;34(4):929-39. Epub 2011 May 4. [Pubmed]

  59. Camargo H; Nusspaumer G; Abia D; Briceño V; Remacha M; Ballesta JP.
    The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2.
    Nucleic Acids Res. 2011 May;39(9):3735-43. Epub 2011 Jan 18. [Pubmed]

  60. 2010

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

  62. 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]

  63. R. Méndez and U.Bastolla
    Torsional Network Model: Normal modes in torsion angle space better correlate with conformation changes in proteins.
    Phys. Rev. Lett.l 2010 228103. [Pubmed]

  64. 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]

  65. Abia D; Bastolla U; Chacón P; Fábrega C; Gago F; Morreale A
    Tramontano A. In memoriam. Angel Ramirez Ortiz (1966-2008).
    Proteins. 2010 78: iii-vii. [Pubmed]

  66. A. Pascual-Garcia; D. Abia; R. Méndez; G.S. Nido and U. Bastolla
    Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation.
    Proteins. 2010 78:181-96 . [Pubmed]

  67. Schaffner-Barbero C; Gil-Redondo R; Ruiz-Avila LB; Huecas S; Läppchen T; den Blaauwen T; Diaz JF; Morreale A; Andreu JM.
    Insights into Nucleotide Recognition by Cell Division Protein FtsZ from a mant-GTP Competition Assay and Molecular Dynamics.
    Biochemistry. 2010 Dec 14;49(49):10458-10472. [Pubmed]

  68. Scheper J; Guerra-Rebollo M; Sanclimens G; Moure A; Masip I; González-Ruiz D; Rubio N; Crosas B; Meca-Cortés O; Loukili N; Plans V; Morreale A; Blanco J; Ortiz AR; Messeguer A; Thomson TM.
    Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation.
    PLoS One. 2010 Jun 30;5(6):e11403. [Pubmed]

  69. Pino-Angeles A; Morreale A; Negri A; Sánchez-Jiménez F; Moya-García AA.
    Substrate uptake and protein stability relationship in mammalian histidine decarboxylase.
    Proteins. 2010;78:154-61. [Pubmed]

  70. Gil-Redondo R; Klett J; Gago F; Morreale A.
    gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.
    Proteins. 2010 Jan;78(1):162-72. [Pubmed]

  71. Arechaga I; Swamy M; Abia D; Schamel WA; Alarcón B; Valpuesta JM.
    Structural characterization of the TCR complex by electron microscopy.
    Int Immunol. 2010 Nov;22(11):897-903. [Pubmed]

  72. Bermudo R; Abia D; Benitez D; Carrió A; Vilella R; Ortiz AR; Thomson TM; Fernández PL.
    Discovery of genomic alterations through coregulation analysis of closely linked genes: a frequent gain in 17q25.3 in prostate cancer.
    Ann N Y Acad Sci. 2010 1210:17-24. [Pubmed]

  73. Jorge-Finnigan A; Aguado C; Sánchez-Alcudia R; Abia D; Richard E; Merinero B; Gámez A; Banerjee R; Desviat LR; Ugarte M; Pérez B.
    Functional and structural analysis of five mutations identified in methylmalonic aciduria cblB type.
    Hum Mutat. 2010;31:1033-42. [Pubmed]

  74. López-Huertas MR; Callejas S; Abia D; Mateos E; Dopazo A; Alcamí J; Coiras M.
    Modifications in host cell cytoskeleton structure and function mediated by intracellular HIV-1 Tat protein are greatly dependent on the second coding exon.
    Nucleic Acids Res. 2010 Jun;38(10):3287-307. [Pubmed]

  75. Martín V; Abia D; Domingo E; Grande-Pérez A.
    An interfering activity against lymphocytic choriomeningitis virus replication associated with enhanced mutagenesis.
    J Gen Virol. 2010 Apr;91(Pt 4):990-1003. [Pubmed]

  76. 2009

  77. Bastolla, U.; Fortuna, M.A.; Pascual-Garcia, A.; Ferrera, A.; Luque, B. and Bascompte, J.
    The architecture of mutualistic networks minimizes competition and increases biodiversity.
    Nature, 458, 1018-1020. [Pubmed] [PDF]

  78. Pascual-Garcia, A.; Abia, D.; Ortiz, A.R. and Bastolla, U.
    Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.
    PLoS Comput Biol, 5, e1000331. [Pubmed] [PDF]

  79. Martinez-Martin, N.; Risueno, R.M.; Morreale, A.; Zaldivar, I.; Fernandez-Arenas, E.; Herranz, F.; Ortiz, A.R. and Alarcon, B.
    Cooperativity between T cell receptor complexes revealed by conformational mutants of CD3epsilon.
    Sci Signal, 2, ra43. [Pubmed] [PDF]

  80. Moya-García, A.A.; Pino-Angeles, A.; Gil-Redondo, R.; Morreale, A. and Sanchez-Jimenez, F.
    Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition.
    Br J Pharmacol, 157, 4-13. [Pubmed] [PDF]

  81. Maria Rodriguez-Mateos; David Abia; Juan J. Garcia-Gomez; Antonio Morreale; Jesus de la Cruz; Cruz Santos; Miguel Remacha; Juan P. G. Ballesta
    The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein.
    Nucleic Acids Research Advance Access. April 3, 2009 [Pubmed] [PDF]

  82. Gil-Redondo, R.; Estrada, J.; Morreale, A.; Herranz, F.; Sancho, J.; Ortiz, A. R.
    VDSMIP: virtual screening data management on an integrated platform.
    J Comput Aided Mol Des. 2009, 23: 171-184 [Pubmed] [PDF]

  83. 2008

  84. 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]

  85. 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]

  86. 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]

  87. Ruiz, F.; Gil-Redondo, R.; Morreale, A.; Ortiz, A.R.; FAbrega, C.; Bravo, J.
    Structure-Based Discovery of novel non-nucleosidic DNA Alkyltransferase inhibitors: virtual screening and in vitro and in vivo activities.
    J Chem Inf Model 2008, 48:844-854 [Pubmed] [PDF]

  88. 2007

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

  90. García Marcos, A.; Morreale, A.; Guarinos, E.; Briones, E.; Remacha, M.; Ortiz, A.R.; P.G.Ballesta,
    J.In vivo assembling of bacterial ribosomal protein L11 into yeast reibosomes makes the particles sensitive to the prokaryotic specific antibiotic thriostrepton.
    Nucleic Acid Research [Pubmed] [PDF]

  91. Hurtado, M.; Lozano, J. J,; Castellanos, E.; Lopez-Fernandez, L. A.; Harshman. K.; Martinez-A, C,; Ortiz, A. R. Thomson, T. M.; Paciucci,
    R.Activation of the epidermal growth factor signalling pathway by tissue plasminogen activator in pancreas cancer cells.
    Gut. 2007 Sep; 56 (9):1266-74 [Pubmed]

  92. 55-. León, E; Yee, A.;Ortiz, A.R.; Santoro, J.; Rico, M.; Jiménez, M.A.
    Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two-layer sandwich architecture.
    Protein Sci. 2007, 16: 2278-86 [Pubmed] [PDF]

  93. Morreale, A.; Gil-Redondo, R.; Ortiz, A.R.
    A new implicit solvent model for protein-ligand docking.
    Proteins 2007 May, 67: 606-16. [Pubmed] [PDF] [Material suplementario]

  94. 2006

  95. 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 May 31. [Pubmed] [PDF]

  96. Bastolla, U.; Demetrius, Ll,
    Stability contraints and protein evolution: the role of chain lenght, composition and disulfide bonds.
    Protein Eng. Des, Sel. 2005 Sep; 18(9): 405-15. [Pubmed] [PDF]

  97. Arias-Pérez, M.S.; Cosme, A.; Gálvez, E.; Morreale, A.; Sanz-Aparicio, J.; Fonseca, I.
    Structural study of () ethyl 3-acyloxy-1-azabicyclo [2.2.2.] octane-3-carboxylates by H, C NMR spectroscopy, X-ray crystallography and DFT calculations.
    Journal of Mol Structure 2006, 789: 71-80.[PDF]

  98. Talavera, D.; Morreale, A.; Meyer, T.; Hospital, A.; Ferrer-Costa, C.; Gelpi, J.Ll.; La Cruz, X. de; Soliva, R.; Luque, F. J.; Orozco, M.
    A fast method for the determintation of fractional contributions to solvation in proteins.
    Protein Sci. 2006 Nov; 15(11): 2525-33. [Pubmed] [PDF]

  99. Murcia, M.; Morreale, A.; Ortiz, A.R.
    Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets.
    J.Med.Chem. 2006 Oct 19; 49 (21): 6241-53. [Pubmed] [PDF] [Material suplementario]

  100. Martin, M.; Perales, C.; Abia, D.; Ortiz, A.R.; Domingo, E.; Briones, C.
    Microarray-based indentification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment.
    BMC Genomics. 2006 May 18;7(1):117. [Pubmed] [PDF] [Material suplementario]

  101. Schamel, W.W.; Risueno, R.M.; Minguet, S.; Ortiz, A.R.; Alarcón, B.
    A conformation- and avidity-based proofreading mechanism for the TCR-CD3 complex.
    Trends Immunol. 2006 Apr; 27(4):176-82. [Pubmed] [PDF]

  102. Ortiz, A.R.; Gómez-Puertas, P.; Leo-Macías, A.; L&oacutepez-Romero, P.; Lopez-Viñas, E.; Morreale, A.; Murcia, M.; Wang, K.
    Computational approaches to model ligand selectivity in drug design.
    Curr Top Med Chem. 2006; 6(1):41-55. [Pubmed] [PDF]

  103. 2005

  104. Lozano, JJ.; Soler, M.; Bermudo, R.; Abia, D.; Fernandez, PL.; Thomson, TM.; Ortiz, A.R.
    Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data.
    BMC Genomics (2005) 6, 109. [Pubmed] [PDF]

  105. Lupyan, D.; Leo-Macias, A.; Ortiz, A.R.
    A new progressive-iterative algorithm for multiple structure alignment.
    Bioinformatics (2005) 21, 3255-63. [Pubmed] [PDF]

  106. Leo-Macias, A.; Lopez-Romero, P.; Lupyan, D.; Zerbino, D.; Ortiz, A.R.
    Core deformations in protein families: a physical perspective. Biophys Chem (2005) 115, 125-8. [Pubmed] [PDF]

  107. Leo-Macias, A.; Lopez-Romero, P.; Lupyan, D.; Zerbino, D. ; Ortiz, A.R.
    An analysis of core deformations in protein superfamilies.
    Biophys J (2005) 88, 1291-9. [Pubmed] [PDF]

  108. 2004

  109. Qian, B.; Ortiz, AR.; Baker, D.
    Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
    Proc Natl Acad Sci U S A (2004) 101, 15346-51. [Pubmed] [PDF]

  110. Wang, K.; Murcia, M.; Constans, P.; Pérez, C.; Ortiz, A.R.
    Gaussian mapping of chemical fragments in ligand binding sites.
    J Comput Aided Mol Des (2004) 18, 101-18. [Pubmed] [PDF]

  111. Blanco, FJ.; Yee, A.; Campos-Olivas, R.; Ortiz, A.R.; Devos, D.; Valencia, A.; Arrowsmith, CH.; Rico, M.
    Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold.
    Protein Sci (2004) 13, 1458-65. [Pubmed] [PDF]

  112. Murcia, M.; Ortiz, AR.
    Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors.
    J Med Chem (2004) 47, 805-20. [Pubmed] [PDF]

  113. 2003

  114. Fischer, D.; Rychlewski, L.; Dunbrack, RL.; Ortiz, A.R.; Elofsson, A.
    CAFASP3: the third critical assessment of fully automated structure prediction methods.
    Proteins (2003) 53 Suppl 6, 503-16. [Pubmed] [PDF]

  115. Sanchez-Carbayo, M.; Socci, ND.; Lozano, JJ.; Li, W.; Charytonowicz, E.; Belbin, TJ.; Prystowsky, MB.; Ortiz, A.R.; Childs, G. ; Cordon-Cardo, C.
    Gene discovery in bladder cancer progression using cDNA microarrays.
    Am J Pathol (2003) 163, 505-16. [Pubmed] [PDF]

  116. 2002

  117. Ortiz, A.R.; Strauss, CE.; Olmea, O.
    MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.
    Protein Sci (2002) 11, 2606-21. [Pubmed] [PDF]

  118. De Las Rivas, J.; Lozano, JJ.; Ortiz, A.R.
    Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Res (2002) 12, 567-83. [Pubmed] [PDF]

  119. 2001

  120. Fischer, D.; Elofsson, A.; Rychlewski, L.; Pazos, F.; Valencia, A.; Rost, B.; Ortiz, A.R.; Dunbrack, RL.
    CAFASP2: the second critical assessment of fully automated structure prediction methods.
    Proteins (2001) Suppl 5, 171-83. [Pubmed] [PDF]

  121. Pérez, C.; Ortiz, A.R. Evaluation of docking functions for protein-ligand docking.
    J Med Chem (2001) 44, 3768-85. [Pubmed] [PDF]

  122. Kmunícek, J.; Luengo, S.; Gago, F.; Ortiz, A.R.; Wade, RC.; Damborský, J.
    Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
    Biochemistry (2001) 40, 8905-17. [Pubmed] [PDF]

  123. Fàbrega, C.; Farrow, M.A.; Mukhopadhyay, B.; de Crécy-Lagard, V.; Ortiz, A.R.; Schimmel, P.
    An aminoacyl tRNA synthetase whose sequence fits into neither of the two known classes.
    Nature (2001) 411, 110-4. [Pubmed] [PDF]

  124. 2000

  125. Swairjo, M.A.; Morales, A.J. ; Wang, C.C.; Ortiz, A.R.; Schimmel, P.
    Crystal structure of trbp111: a structure-specific tRNA-binding protein.
    EMBO J (2000) 19, 6287-98. [Pubmed] [PDF]

  126. Ortiz, AR.; Skolnick, J.
    Sequence evolution and the mechanism of protein folding.
    Biophys J (2000) 79, 1787-99. [Pubmed] [PDF]

  127. Simmerling, C.; Lee, M. L.; Ortiz, A.R.; Kolinski, A.; Skolnick, J.; Kollman, P.A.
    Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1 J.
    Am. Chem. Soc. (2000) 122, 8392-8402.[Pubmed] [PDF]

  128. Skolnick, J; j Kolinski, A.; Ortiz, A.R.
    Derivation of Protein-Specific Pair Potentials Based on Weak Sequence Fragment Similarity.
    Proteins (2000) 38, 3–16. [Pubmed] [PDF]

  129. 1999

  130. Ortiz, A.R.; Kolinski, A.; Rotkiewicz, P.; Ilkowski, B.; Skolnick, J.
    Ab initio folding of proteins using restraints derived from evolutionary information.
    Proteins (1999) Suppl 3, 177-85. [Pubmed] [PDF]

  131. Rodriguez, Esteban C.; Capdevila J.; Economides A.N.; Pascual J.; Ortiz, A.R.; Izpisua, Belmonte J.C.
    The novel Cer-like protein Caronte mediates the establishment of embryonic left-right asymmetry.
    Nature (1999) 401, 222-3. [Pubmed] [PDF]

  132. 1998

  133. Skolnick, J.; Kolinski, A.; Ortiz, AR.
    Reduced protein models and their application to the protein folding problem. J Biomol Struct Dyn (1998) 16, 381-96. [Pubmed] [PDF]

  134. Ortiz, AR.; Kolinski, A.; Skolnick, J.
    Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins.
    Pac Symp Biocomput (1998) , 377-88. [Pubmed] [PDF]

  135. Ortiz, AR.; Kolinski, A.; Skolnick, J.
    Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.
    J Mol Biol (1998) 277, 419-48. [Pubmed] [PDF]

  136. Pérez, C.; Pastor, M.; Ortiz, AR.; Gago, F.
    Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.
    J Med Chem (1998) 41, 836-52. [Pubmed] [PDF]

  137. Ortiz, AR.; Kolinski, A.; Skolnick, J.
    Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments.
    Proteins (1998) 30, 287-94 [Pubmed] [PDF]

  138. Ortiz, AR.; Kolinski, A.; Skolnick, J.
    Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations.
    Proc Natl Acad Sci U S A (1998) 95, 1020-5. [Pubmed] [PDF]

  139. 1997

  140. Checa, A.; Ortiz, AR.; de Pascual-Teresa, B.; Gago, F.
    Assessment of solvation effects on calculated binding affinity differences: trypsin inhibition by flavonoids as a model system for congeneric series.
    J Med Chem (1997) 40, 4136-45 [Pubmed] [PDF]

  141. Ortiz, AR.; Hu, WP.; Kolinski, A.; Skolnick, J.
    Method for low resolution prediction of small protein tertiary structure.
    Pac Symp Biocomput (1997) , 316-27. [Pubmed] [PDF]

  142. Blanco, FJ.; Ortiz, AR.; Serrano, L.
    1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: comparison of unrefined and refined structure sets with the crystal structure.
    J Biomol NMR (1997) 9, 347-57. [Pubmed] [PDF]

  143. Ortiz, AR.; Pastor, M.; Palomer, A.; Cruciani, G.; Gago, F.; Wade, RC.
    Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors.
    J Med Chem (1997) 40, 1136-48. [Pubmed] [PDF]

  144. Gallego, J.; Ortiz, AR.; de Pascual-Teresa, B.; Gago, F.
    Structure-affinity relationships for the binding of actinomycin D to DNA.
    J Comput Aided Mol Des (1997) 11, 114-28. [Pubmed] [PDF]

  145. Skolnick, J.; Kolinski, A.; Ortiz, AR.
    MONSSTER: a method for folding globular proteins with a small number of distance restraints.
    J Mol Biol (1997) 265, 217-41. [Pubmed] [PDF]

  146. Blanco, FJ.; Ortiz, AR.; Serrano, L.
    Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational analysis of the alpha-helix fragment.
    Fold Des (1997) 2, 123-33. [Pubmed] [PDF]

  147. 1996

  148. Magrans,J.O; Ortiz, A.R.; Molins, A.; Lebouille, P.H.P.; Sanchez-Quesada, J.; Pons, M.; Gago, F.; de Mendoza, J.
    A designed non-peptidic receptor that mimics the phosphocoline binding site of the McPC603 antibody.
    Angew.Chem.Int.Ed.Eng. (1996) 35, 2712-1715.[Pubmed] [PDF]

  149. de Pascual-Teresa, B.; Gallego, J.; Ortiz, AR.; Gago, F.
    Molecular dynamics simulations of the bis-intercalated complexes of ditercalinium and Flexi-Di with the hexanucleotide d(GCGCGC)2: theoretical analysis of the interaction and rationale for the sequence binding specificity.
    J Med Chem (1996) 39, 4810-24: [Pubmed] [PDF]

  150. 1995

  151. Ortiz, AR.; Pisabarro, MT.; Gago, F.; Wade, RC.
    Prediction of drug binding affinities by comparative binding energy analysis.
    J Med Chem (1995) 38, 2681-91. [Pubmed] [PDF]

  152. 1994

  153. Pisabarro, MT.; Ortiz, AR.; Viguera, AR.; Gago, F.; Serrano, L.
    Molecular modeling of the interaction of polyproline-based peptides with the Abl-SH3 domain: rational modification of the interaction.
    Protein Eng (1994) 7, 1455-62. [Pubmed] [PDF]

  154. Pisabarro, MT.; Ortiz, AR.; Serrano, L.; Wade, RC.
    Homology modeling of the Abl-SH3 domain.
    Proteins (1994) 20, 203-15. [Pubmed] [PDF]

  155. Pisabarro, MT.; Ortiz, AR.; Palomer, A.; Cabré, F.; García, L.; Wade, RC.; Gago, F.; Mauleón, D.; Carganico, G.
    Rational modification of human synovial fluid phospholipase A2 inhibitors.
    J Med Chem (1994) 37, 337-41. [Pubmed] [PDF]

  156. 1993

  157. Ortiz, AR.; Pisabarro, MT.; Gago, F.
    Molecular model of the interaction of bee venom phospholipase A2 with manoalide.
    J Med Chem (1993) 36, 1866-79. [Pubmed] [PDF]

  158. Gallego, J.; Ortiz, AR.; Gago, F.
    A molecular dynamics study of the bis-intercalation complexes of echinomycin with d(ACGT)2 and d(TCGA)2: rationale for sequence-specific Hoogsteen base pairing.
    J Med Chem (1993) 36, 1548-61. [Pubmed] [PDF]

  159. Minguez, J.M.; Gandasegui, T.; Vaquero, J.J.; Alvarez-Builla, J.; Garcia-Navio, J.L; Gago, F.; Ortiz, A.R.; Gomez-Sal, P.; Torres, R.; Rodrigo, M.
    New 3-(2'-benzimidazolyl) imidazo [1,2-a] pyridinium mesomeric betaines. Synthesis and structure.
    J. Org. Chem. (1993) 58, 6030-6037.[Pubmed] [PDF]

  160. 1992

  161. Ortiz, AR.; Pisabarro, MT.; Gallego, J.; Gago, F.
    Implications of a consensus recognition site for phosphatidylcholine separate from the active site in cobra venom phospholipases A2.
    Biochemistry (1992) 31, 2887-96. [Pubmed] [PDF]

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