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Publications on molecular modeling

  1. 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]

  2. 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]

  3. 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]

  4. 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]

  5. 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]

  6. 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]

  7. 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]

  8. 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]

  9. 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]

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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]

  15. 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]

  16. 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]

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

  18. 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]

  19. 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]

  20. 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]

  21. 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]

  22. 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]

  23. 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]

  24. 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]

  25. 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]

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

  27. 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]

  28. 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]

  29. 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]

  30. 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]

  31. 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]

  32. 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]

  33. 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]

  34. 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]

  35. 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]

  36. 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]

  37. 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]

  38. 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]

  39. 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]

  40. 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]

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

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