Submitted


In Press

67- María Rodríguez-Mateos; David Abia; Juan J. García-Gómez; Antonio Morreale; Jesús 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 Acid Research 2009(in press)

66- Moya-García, A. A.; Pino-Ángeles, A .; Gil-Redondo, R.; Morreale, A.; Sánchez-Jiménez, F.
Structural features of mammalian histidine decarboxylase reveal the bases for specific inhibition.
British J Pharmacology 2009 (in press)

65- Pascual-García, A.; Abia, D .; Ortiz, A. R; Bastolla, U.
Cross-over between discrete and continuous protein structure space: Insights into automatic classification and networks of protein structures.
PLoS Comput Biol 2009 (in press)

Published
2009

64- Maria Rodriguez-Mateos; David Abia; Juan J. Garcia-Gomez; Antonio Morreale; Jesus de la Cruz; Cruz Santos; Miguel Remacha; Juan P. G. Ballesta
VDSMIP: 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]

63- 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]

2008

62- 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]

61- 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]

60- 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]

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

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

57- 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]

56-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]

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]

54- 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] [Suplementary material]

2006

53- 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]

52- 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]

51- Bastolla, U; Porto, M.; Román, 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]

50- 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]

49- 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] [Suplementary material]

48- 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] [Suplementary material]
47- 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]
46- Ortiz, A.R.; Gómez-Puertas, P.; Leo-Macías, A.; López-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]
2005
45- 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]

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

43- 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]

42- 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]

2004
41- 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]

40- 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]

39- 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]

38- 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]

2003
37- 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]

36- 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]

2002
35- 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]

34- 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]

2001
33- 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]

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

31- 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]

30- 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]

2000
29- 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]
28- 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]
26- 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]
1999
25- 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]

24- 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]
1998
23- 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]

22- 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]

21- 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]

20- 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]

19- 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]
18- 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]
1997
17- 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]
16- 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]

15- 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]

14- 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]

13- 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]

12- 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]

11- 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]

1996

10- 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]

9- 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]

1995
8- 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]

1994
7- 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]

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

5- 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]

1993
4- 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]

3- 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]

2- 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]
1992
1- 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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