Home Publications


E-mail Print PDF

Group publications since 2001

  1. Leoni G, Tramontano A. A structural view of microRNA–target recognition. Nucl.Acids Res. (2016). doi: 10.1093/nar/gkw043. [Epub ahead of print]

  2. Milanetti E, Raimondo D, Tramontano A. Prediction of the permeability of neutral drugs inferred from their solvation properties.  Bioinformatics. 2015 Dec 10. pii: btv725. [Epub ahead of print]

  3. Messih M.A., Lepore R., Tramontano A. LoopIng: a template-based tool for predicting the structure of protein loops. Bioinformatics (2015) 31 (23): 3767-3772. doi: 10.1093/bioinformatics/btv438

  4. Bonome E., Lepore R., Raimondo D., Cecconi F., Tramontano A., Chinappi M. Multistep current signal in protein translocation through graphene nanopores.  The Journal of Physical Chemistry B. 2015 May 7;119(18):5815-23. doi: 10.1021/acs.jpcb.5b02172

  5. S. Bonella, D. Raimondo, E. Milanetti, A. Tramontano, and G. Ciccotti. Mapping the Hydropathy of Amino Acids Based on Their Local Salvation Structure. J. Phys. Chem. B, 2014, 118 (24), pp 6604–6613. DOI: 10.1021/jp500980x

  6. Ballarino M, Cazzella V, D'Andrea D, Grassi L, Bisceglie L, Cipriano A, Santini T, Pinnarò C, Morlando M, Tramontano A and Bozzoni I: Novel lncrnas in myogenesis: a mir-31 overlapping transcript controls myoblast differentiation. Molecular and Cellular Biology (2014) MCB–01394

  7. Domina M, Cariccio V L, Benfatto S, D'Aliberti D, Venza M, Borgogni E, Castellino F, Biondo C, D'Andrea D, Grassi L, Tramontano A, Teti G, Felici F and Beninati C: Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries. PloS one 9(12) (2014) e114159

  8. Olimpieri PP, Marcatili P and Tramontano A. Tabhu: Tools for antibody humanization. Bioinformatics. 2015 Feb 1;31(3):434-5. doi: 10.1093/bioinformatics/btu66

  9. Marcatili P, Olimpieri PP, Chailyan A, Tramontano A. Antibody structural modeling with PIGS. Nature Protocols.9, 2771-2783, doi:10.1038/nprot.2014.189 (2014).

  10. Dias RO, Via A, Brandão MM,Tramontano A, Silva-Filho MC. Digestive Peptidase Evolution in Holometabolous Insects Led to a Specialized Group of Enzymes in Lepidoptera. Insect Biochem Mol Biol. 2015 Mar;58:1-11. doi: 10.1016/j.ibmb.2014.12.009

  11. Di Marino D, Coletta A, D'Annessa I, Via A, Tramontano A. Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. falciparum Ca2+ pumps: a computational study. Proteins. 2015 Mar;83(3):564-74. doi: 10.1002/prot.24734

  12. Messih MA, Lepore R, Marcatili P, Tramontano A. (2014) Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chain of antibodies. Bioinformatics. 2014 Oct;30(19):2733-40. doi: 10.1093/bioinformatics/btu194

  13. Fiorillo A, di Marino D, Bertuccini L, Via A, Pozio E, Camerini S, Ilari A, Lalle M. The crystal structure of Giardia duodenalis 14-3-3 in the apo form: when protein post-translational modifications make the difference (2014) PLoS One 9(3):e92902. doi: 10.1371/journal.pone.0092902. eCollection 2014.

  14. D'Andrea, D., Grassi, L., Mazzapioda, M. and Tramontano, A. FIDEA: a server for the functional interpretation of differential expression analysis Nucl. Acids Res. (1 July 2013) 41 (W1)

  15. Lepore R, Tramontano A, Via A. TiPs: a database of therapeutic targets in pathogens and associated tools (2013) Bioinformatics 29(14):1821-2. doi: 10.1093/bioinformatics/btt289.

  16. Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. Best practices in bioinformatics training for life scientists (2013) Brief Bioinform. 14(5):528-37. doi: 10.1093/bib/bbt043.

  17. Olimpieri, P.P., Chailyan, A., Tramontano, A. and Marcatili, P. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. Bioinformatics, 29, 2285-2291, doi:10.193/bioinformatics/btt369 (2013)

  18. Marcatili, P., Ghiotto, F., Tenca, C., Chailyan, A., Mazzarello, A. N., Yan, X., Colombo, M., Albesiano, E., Bagnara, D., Cutrona, G., Morabito, F., Bruno, S., Ferrarini, M., Chiorazzi, N., Tramontano, A., and Fais, F.  Immunoglobulins expressed by chronic lymphocytic leukemia B cells show limited binding site structure variability. J Immunol. 2013 Jun 1;190(11):5771-8. doi: 10.4049/jimmunol.1300321

  19. Kosinski, J., Barbato, A., Tramontano, A. MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. Bioinformatics. 2013 Apr 1;29(7):953-4. doi: 10.1093/bioinformatics/btt062.

  20. Cicconardi, F., Chillemi, G., Tramontano, A. Marchitelli, C., Valentini, A., Ajmone-Marsan, P. and Nardone. A. Massive screening of copy number population-scale variation in Bos taurus genome. BMC Genomics. 2013 Feb 26;14:124. doi: 10.1186/1471-2164-14-124.

  21. Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M. iAnn: an event sharing platform for the life sciences (2013) Bioinformatics 29(15):1919-21, doi: 10.1093/bioinformatics/btt306.

  22. Bottini, S., Bernini, A., De Chiara, M., Garlaschelli, D., Spiga, O., Dioguardi, M., Vannuccini, E, Tramontano, A., and Niccolai, N. ProCoCoA: a quantitative approach for analyzing protein core composition Computational Biology and Chemistry (2013) 43: 29–34, doi:10.1016/j.compbiolchem.

  23. Lacivita E., Patarnello D., Stroth N., Caroli A., Niso M., Contino M., De Giorgio P., Di Pilato P., Colabufo N., Berardi F., Perrone R., Svenningsson P., Hedlund P., and Leopoldo M., Investigations on the 1-(2-Biphenyl)piperazine Motif: Identification of New Potent and Selective Ligands for the Serotonin7 (5-HT7) Receptor with Agonist or Antagonist Action in Vitro or ex Vivo. , J. Med. Chem., 2012, 55 (14), pp 6375–6380

  24. Carbajo, D. and Tramontano, A. A resource forbenchmarking the usefulness of protein structure models. BMCBioinformatics (2012) 13:188.

  25. Sanchez, C. and Tramontano, A. Detecting Mutually Exclusive Interactions in Protein-Protein Interaction Maps. PLoS One (2012) 7(6) e38765doi:10.1371/journal.pone.0038765

  26. Magnacca A., Persiconi I., Nurzia E., Caristi S., Meloni F., Barnaba V., Paladini F., Raimondo D., Fiorillo MT, and Sorrentino R. Characterization of a proteasome and TAP-independent presentation of intracellular epitopes by HLA-B27 molecules. J Biol Chem. 2012 Aug 31;287(36):30358-67. doi: 10.1074/jbc.M112.384339.

  27. Doti N., Raimondo D., Marco Sabatella M. and Ruvo M.Identification of protease inhibitorsa by a fast· fluorimetric assay·. Mol Biotechnol. 2012 Jun.

  28. Romano V., Raimondo D.,Calvanese L., Gabriella D’Auria G., Tramontano A. and Falcigno· l. Toward a better understanding of the interaction between TGF-b family members and their ALK receptors. J Mol Model,·2012 Feb 22

  29. Pillai D.R., Lau R., Khairnar K., Lepore R., Via A., Staines H.M., Krishna S. (2012) Artemether resistance in vitro is linked to mutations in PfATP6 in travellers returning with Plasmodium falciparum infections. Malar J. 11(1):131

  30. Barbato, A., Benkert, P., Schwede, T., Tramontano, A., Kosinski J. Improving your target-template alignment with MODalign. (2012) Bioinformatics, doi: 10.1093/bioinformatics/bts070

  31. Chailyan, A., Tramontano, A., Marcatili, P. A database of immunogloblins with integrated tools: DIGIT Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr806

  32. Caroli A., Simeoni S., Lepore R., Tramontano A., Via A. (2011) Investigation of a Potential Mechanism for the Inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum Inhibition. Biochem Biophys Res Commun. 2012 Jan 6;417(1):576-81. doi: 10.1016/j.bbrc.2011.12.009.

  33. Dinkel H., Michael S., Weatheritt R.J., Davey N.E., Van Roey K., Altenberg B., Toedt G., Uyar B., Seiler M., Budd A., Jödicke L., Dammert M.A., Schroeter C., Hammer M., Schmidt T., Jehl P., McGuigan C., Dymecka M., Chica C., Luck K., Via A., Chatr-Aryamontri A., Haslam N., Grebnev G., Edwards R.J., Steinmetz M.O., Meiselbach H., Diella F., Gibson T.J. (2012) ELM--the database of eukaryotic linear motifs. Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51. doi: 10.1093/nar/gkr1064.

  34. Schneider M.V., Walter P., Blatter M.C., Watson J., Brazas M.D., Rother K., Budd A., Via A., van Gelder C.W.G., Jacob J., Fernandes P., Nyronwn T., De Las Rivas J., Blicher T., Loveland J., McDowall J., Jones P., Bren Vaughan, Lopez R., Attwood T.K., Brooksbank C. (2011) Bioinformatics Training Network (BTN): A community resource for bioinformatics trainers. BriefBioinform (2011) doi: 10.1093/bib/bbr064.

  35. Cesana, M., Cacchiarelli, D., Legnini, I., Santini, T., Sthandier, O., Chinappi, M., Tramontano, A. and Bozzoni, I. A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA. (2011) Cell 147, 358–369.

  36. Grassi L., Tramontano, A. (2011) Horizontal and vertical growth of S. cerevisiae metabolic network. BMC Evol Biol. 2011 Oct 14;11:301. doi: 10.1186/1471-2148-11-301.

  37. Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round IX. Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200.

  38. Monastyrskyy, B.,  Fidelis, K.,   Moult, J.,   Tramontano, A. and  Kryshtafovych, A. (2011) Evaluation of model quality predictions in CASP9, Proteins, in press.

  39. Lepore R., Simeoni S., Raimondo D., Caroli A., Tramontano A., Via A. (2011) Identification of the Schistosoma mansoni Molecular Target for the Anti Malarial Drug Artemether. J Chem Inf Model. 51(11):3005-16.

  40. Sayadi A, Briganti L, Tramontano A, Via A (2011) Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PLoS One. 2011;6(7):e22270.

  41. Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JAM, et al. (2011) Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Comput Biol 7(10): e1002245. doi:10.1371/journal.pcbi.1002245.

  42. Ghiotto, F.  Marcatili, P.  Tenca, C.,  Calevo, M.G.,  Yan, X., Albesiano, E.,  Bagnara, D.  Colombo, M.,  Cutrona, G.,   Chu, C.C., Morabito, F.,  Bruno, S.  Ferrarini, F.,   Tramontano, A.  Fais, F.,and  Chiorazzi, N. (2011) Analysis of mutation patterns of paired immunoglobulin heavy and light variable domains expressed by chronic lymphocytic leukemia B cells. Mol Med. 2011;17(11-12):1188-95. doi: 10.2119/molmed.2011.00104.

  43. Kryshtafovych, A.,   Fidelis, K. and Tramontano, A. (2011) Evaluation of residue-residue contacts predictions in CASP9. Proteins. 2011;79 Suppl 10:119-25. doi: 10.1002/prot.23160.

  44. Monastyrskyy, B.,   Fidelis, K.,   Moult, J.,   Tramontano, A. and  Kryshtafovych, A. Evaluation of disorder prediction in CASP9. Proteins. 2011;79 Suppl 10:107-18. doi: 10.1002/prot.23161..

  45. Chailyan A, Marcatili P., Tramontano A (in press). The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. THE FEBS JOURNAL, ISSN: 1742-464X, doi: 10.1111/j.1742-4658.2011.08207.x

  46. Via A, Tramontano A (2011) Protein structural motifs: identification, annotation and use in function prediction. In "Sequence and Genome Analysis: Methods and Application II", iConcept Press Ltd. Australia.

  47. Eberini, I.,  Emerson, A.,  Sensi, C.,  Ragona, L.,  Ricchiuto, P.,  Pedretti, A.,  Gianazza, E. and  Tramontano, A. (2011) Simulation of urea-induced protein unfolding: A lesson from BOVINE β-lactoglobulin. Journal of Molecular Graphics and Modelling, doi:10.1016/j.jmgm.2011.06.004

  48. Ko WY, Kaercher KA, GiombiniI E, MarcatiliI P., Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Ranciaro A, Hirbo JB, Tishkoff SA (2011). Effects of Natural Selection and Gene Conversion on the Evolution of Human Glycophorins Coding for MNS Blood Polymorphisms in Malaria-Endemic African Populations. AMERICAN JOURNAL OF HUMAN GENETICS, vol. 88; p. 741-754, ISSN: 0002-9297, doi: 10.1016/j.ajhg.2011.05.005

  49. Floris, M., Raimondo, D., Leoni, G., Orsini, M., Marcaili, P. amd Tramontano, A. MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics,79(5) 1513–1524

  50. Valente, S., Tardugno, M., Conte, M., Cirilli, R., Perrone, A., Ragno, R., Simeoni, S., Tramontano, A., Massa, S., Nebbioso, A., Miceli, M., Franci, G., Brosch, G., Altucci, L. and Mai, A. (2011) Novel Cinnamyl Hydroxyamides and 2-Aminoanilides as Histone Deacetylase Inhibitors: Apoptotic Induction and Cytodifferentiation Activity, ChemMedChem,4;6(4):698-712. doi: 10.1002/cmdc.201000535

  51. Mancini, E.,  Tammaro,  F.,  Baldini, F.,  Via, A., Raimondo, D.,  George, P.,  Audisio, P.,  Sharakhov, I.V., Tramontano,A.,  Catteruccia, F. and  della Torre, A. (2011) Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract.  BMC Evolutionary Biology11:72doi:10.1186/1471-2148-11-72

  52. Chailyan, A., Marcatili, P., Cirillo D. and Tramontano, A. (2011) Structural repertoire of immunoglobulin λ light chains. PROTEINS, vol. 79-5; p. 1513-1524, ISSN: 0887-3585, doi: 10.1002/prot.22979

  53. Leoni, G., Le Pera, L., Ferre', F., Raimondo, D., Tramontano, A. Coding potential of the products of alternative splicing in human.(2011)  Genome Biology, 12:R9 doi:10.1186/gb-2011-12-1-r9

  54. Chinappi M, Via A, Marcatili P, Tramontano A. (2010) On the Mechanism of Chloroquine Resistance in Plasmodium falciparum. PLoS ONE 5(11): e14064. doi:10.1371/journal.pone.0014064

  55. Schneider MV., Watson J., Attwood T., Rother K., Budd A., McDowall J., Via A., Fernandes P., Nyronen T., Blicher T., Jones P., Blatter M-C., De Las Rivas J., Judge DP.,van der Gool W. and Brooksbank C. (2010) Bioinformatics training: a review of challenges, actions and support requirements. Briefings in Bioinformatics, 11(6): 544-551.

  56. Le Pera, L., Marcatili, P., Tramontano, A. Picmi: mapping point mutations on genomes, Bioinformatics, 26(22): 2904-2905

  57. Zanzoni A., Carbajo D., Diella F., Gherardini P.F., Tramontano A., Helmer-Citterich M., Via A. Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites (2011) Nucleic Acid Research,39:d268-d271 

  58. Raffa GD., Raimondo, D., Sorino C., Cugusi S., Cenci G., Cacchione S., Gatti M. and Ciapponi L. Verrocchio, a Drosophila OB-fold containing protein, is a component of the terminin telomere-capping complex. Genes & Development, (2010) 24(15):1596-601

  59. Zibellini,S. ,  Capello, D.,  Forconi, F.,  Marcatili, P.,  Rossi, D.,  Rattotti, S.,  Franceschetti, S.,  Sozzi, E.,  Cencini, E.,  Marasca, R.,  Baldini, L.,  Tucci,A.,   Bertoni, F.,  Passamonti, F.,  Orlandi, E.,  Varettoni, M.,  Merli, M.,  Rizzi, S.,  Gattei, V.,  Tramontano, A.,  Paulli, M.,  Gaidano, G., and  Arcaini, L. Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma (2010) Haematologica, doi:10.3324/haematol.2010.025437

  60. Giombini, E., Orsini, M., Carabino, D. and Tramontano, A.  An automatic method for identifying surface proteins in bacteria: SLEP (2010) BMC Bioinformatics 2010, 11:39

  61. Maullu, C., Raimondo, D., Caboi, F., Giorgetti, A., Sergi, M., Valentini, M., Tonon, G., Tramontano, A. Site-directed enzymatic PEGylation of the Human Granulocyte Colony Stimulating Factor. (2009) FEBS J.276: 7474-7596

  62. Tramontano, A Bioinformatics. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. (2009) DOI: 10.1002/9780470015902.a0001900.pub2

  63. Tramontano, A. No protein is an island. Current Opin. Struct. Biol. 2009, 19(3): 310-311

  64. Moult, J., Fidelis, K., Kryshtafovych, A., Rost, B. and Tramontano, A. Critical Assessment of Protein Structure Prediction (CASP) - Round VIII. Proteins, (2009) Proteins, 77: 1-4

  65. Cozzetto, D., Kryshtafovych, A. and Tramontano, A. Evaluation of CASP8 Model Quality Predictions. Proteins77: 157-166

  66. Cozzetto, D., Kryshtafovych, A., Fidelis, K., Moult, J., Rost, B. and Tramontano, A. Evaluation of template-based models in CASP8 with standard measures. Proteins, 11:18-28

  67. Loewenstein,Y.,   Raimondo, D.,  Redfern, O.,  Watson, J.  Frishman, D.,  Linial, M.,  Orengo, C.,  Thornton, J.,  Tramontano, A. Protein function annotation by homology-based inference Genome Biology 2009, 10:207.

  68. Tramontano, A., Jones, D., Rychlewski, L.,  Casadio, R. Martelli, P.,  Raimondo, D. and  Giorgetti, A.  In Frishman, D. and Valencia, A. (eds.), Modern genome annotation: the BioSapiens network. Springer. ISBN: 978-3-211-75122-0

  69. Raimondo, D., Giorgetti,A.,  Bernassola,F.,  Melino G., Tramontano, A. Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase Itch and the E2 UbcH7 (2008) Molecular Pharmacology, 76 (11): 1620-1627

  70. Marcatili, P., Rosi, A. and Tramontano, A. PIGS: Automatic prediction of antibody structures (2008) Bioinformatics, 24(17):1953-1954.

  71. Lacal, P.M, Morea, V., Ruffini, F., Orecchia, A., Dorio, A.S., Failla, C. M., Soro, S., Tentori, L., Zambruno, G., Graziani, G., Tramontano, A. and D'atri, S. Inhibition of Endothelial Cell Migration and Angiogenesis by a Vascular Endothelial Growth Factor Receptor-1 derived peptide (2008) Eur. J. Cancer, 4(13): 1914-1921

  72. Soro, S., Orecchia, A., Lacal, P.M., Morea, V., Ballmr-Hofer, K., Ruffini, F., Ziche, M., Zambruno, G., Tramontano, A. and Failla, C.M. (2007) A proangiogenic peptide derived from vascular endothelial growth factor receptor-1 acts through alpha5beta1 integrin (2008) Blood, 111:3479-3488.

  73. Occhino,M., Ghiotto,F., Soro,S., Mortarino, M., Bosi,S., Maffei, M., Bruno,S., Nardini,M., Figini, M., Tramontano,A. and Ciccone, E. Dissecting the Structural Determinants of the Interaction between the Human Cytomegalovirus UL18 Protein and the CD85j Immune Receptor (2008) J. of Immun., 180:957-968.

  74. Ausiello, G., Gherardini, P.F., Marcatili, P., Tramontano, A., Via, A., Helmer-Citterich, M. FunClust: A web server for the identification of structural motifs in a set of non-homologous proteins. (2008) BMC Bioinformatics, 9:S2

  75. Marcatili, P., Bussotti, G., Tramontano, A. The MoVin server (2008) BMC Bioinformatics, 9:S11

  76. Montanari, A., Besagni, C., De Luca, C., Morea, V., Oliva, R., Tramontano, A., Bolotin-Fukuhara, M., Frontali, L. and Francisci, S. Yeast as a model of human mitochondrial tRNA base substitutions: Investigation of the molecular basis of respiratory defects (2008) RNA, 14: 275-283.

  77. Cozzetto, D., Giorgetti, A., Raimondo, D. and Tramontano, A. The evaluation of protein structure prediction results. (2008) Molecular Biotechnology 39: 1-8

  78. Guariento, M., Raimondo, D., Assfalg, M., Zanzoni, S., Pesente, P., Ragona, L., Tramontano, A. and Molinari, H. Identification and functional characterization of the bile acid transport proteins in non-mammalian ileum and mammalian liver. (2008) Proteins, 70: 462-372

  79. Tramontano, A. and Pearson, W.R. The completeness of biological space (2007) Curr. Op. Struct. Biol. 17:334-336

  80. Bryson, K., Cozzetto, D. and Jones D.T. 2007 Computer-assisted Protein Domain Boundary Prediction using the DomPred Server Curr Protein Pept Sci.8: 181-188

  81. Moult, J., Fidelis, K., Kryshtafovych, A., Rost, B., Hubbard, T. and Tramontano, A. Critical Assessment of Protein Structure Prediction (CASP) - Round VII. (2007) Proteins, 8:3-9.

  82. Tramontano, A., Cozzetto, D., Giorgetti, A. and Raimondo R. The assessment of methods for protein structure prediction in Protein structure prediction: methods in Molecular Biology (2007) Vol. 413 pp. 43-57 2nd edition. Edited by Chris Bystroff and Mohammed Zaki; The Humana Press, Inc

  83. Cozzetto, D, Kryshtafovych, A., Ceriani, M. and Tramontano, A. Assessment of predictions in the Model Quality Assessment category. (2007) Proteins, 8:175-183

  84. Oliva, R., Tramontano, A., Cavallo, L. Mg2+ Binding and Archeaeosine Modification stabilize the G15-C48 Levitt base pairs in tRNAs (2007) RNA, 13: 1427-1436.

  85. Carrabino, D., D'Onorio De Meo, P., Sanna, N., Castrignano', T. Orsini, M., Floris, M. and Tramontano, A. The mepsMAP server (2007) IEEE Transactions on nanobiosciences, 6(2),155-161

  86. Bertonati, C., Tramontano, A. A model of the complex between the PfEMP1 Malaria Protein and the Human ICAM-1 Receptor (2007) Proteins, 69(2), 215-222.

  87. Tress, M., Martelli, P.L., Frankish, A., Reeves, G., Wesselink J.J., Yeats, C., Olason, P.I., Albrecht, M., Hegyi H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R., Lopez, G., Sadowski, M.I., Watson, J., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Stoerling, Z., Orsini, M., Assenov, Y., Blakenburg, H., Huthmacher, C., Ramirez, F., Schlicker, A., Denoued, F., Jones, P., Kerrien, S., Orchard, S., Birney, E., Brunak, S., Casadio, R., Guigo, R., Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C., Patthy, L., Thornton, J., Tramontano, A., Valencia, A. The implications of alternative splicing in the ENCODE protein complement. (2007) Proc. Natl. Acad. Sci., 104, 5495-5500

  88. Bianchettin, G., Bonaccini, C., Oliva, R., Tramontano, A., Cividini, A., Casato, M., Merlini, G., Silini, E. and Mondelli, M.U.Analysis of Hepatitis C virus hypervariable region 1 sequence in cryoglobulinemic patients and associate controls (2007) J. Virol. 81, 4564-4571

  89. Ragno, R., Simeoni, S., Castellano, S., Vicidomini, C., Mai, A., Tramontano, A., Bonaccini, C., Trojer, P., Bauer, I. and Sbardella, G. Small molecule inhibitors of histone arginine methyltransferase: homology modeling, molecular docking , binding mode analysis and biological evaluation. (2007) J. Med. Chem. 50, 1241-1253

  90. Tramontano, A. Worth the effort: an account of the Seventh meeting of the worldwide critical assessment of Techniques for Protein Structure Prediction (2007) FEBS J:, 274, 1651-1654.

  91. Castrignano', T., D'Onorio De Meo, P., Carrabino, D., Orsini, M., Floris, M. and Tramontano, A. The MEPS server for identifying protein conformational epitopes, (2007) BMC Bioinformatics 10:1186/1471-2105-8-S1-s&

  92. Kinzel, O., Fattori, D., Muraglia, E., Gallinari, P., Nardi, M.C., Paolini, C., Roscilli, G., Toniatti, C., Gonzales-Paz, O., Laufer, R., Lahm, A., Tramontano, A., Cortese, R., De Frncesco, R. A structure-guided approach to an otthogonla estrogen-receptor-based gene switch activated by ligands suitable for in vivo studies. (2006) J. Med. Chem. 49(18) 5404-5407.

  93. Book: Tramontano, A. Introduction to Bioinformatics CRC Press, New York (2006).

  94. Raimondo, D., Giorgetti, A., Bosi, S. and Tramontano, A. An automatic procedure for using models of proteins in molecular replacement, (2006) Proteins, 66:689-696.

  95. Oliva, R., Cavallo, L. and Tramontano, A. Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions, Nucl. Acids Res. (2006) 34(3), 865-879.

  96. Magnani, M., Ortuso, F., Soro, S., Alcaro, S., Tramontano, A. and Botta, M. The betaI/betaIII tubulin isoforms and their complexes with antimitotic agents: docking and molecular dynamics studies. FEBS J. (2006) 273 (14), 3301-3310.

  97. Pellegrini Calace, M., Soro, S. and Tramontano, A. Revisiting the prediction of protein function at CASP6 FEBS J. (2006) 273, 2977-2983.

  98. Tress, M., Cozzetto, D., Tramontano, A. and Valencia, A. An analysis of the Sargasso See Resource and the consequences of database composition BMC Bioinformatics (2006) 7, 213.

  99. Tramontano, A. The role of molecular modelling in biomedical research (2006) FEBS Lett., 580 (12), 2928-2934.

  100. Pellegrini-Calace, M. and Tramontano, A. Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches. (2006) Bioinformatics, 22, 775-778

  101. Gianazza, E., Vergani, L., Brizio, C., Brambilla, D., Begum, S., Giancaspero, T.A., Conserva, F., Eberini, I., Angelini, C., Pegoraro, E., Tramontano, A. and Barile, M. (2006) Coordinated and reversible reduction of enzymes involved in oxidative metabolism in skeletal muscle mitochondria from a riboflavin-responsive, multiple acyl-CoA dehydrogenase deficiency (RR-MAD) patient Electrophoresis, 27 1182-1198.

  102. Book: Tramontano, A. 2006. Protein Structure Prediction, Wiley Inc. Weinheim, Germany.

  103. Tramontano, A. Bioinformatica, XXI Secolo - Aggiornamento dell'Enciclopedia italiana di scienze, lettere ed arti, Treccani, 2006 .

  104. Castrignano', T., D'Onorio De Meo, P., Cozzetto, D., Talamo, I. and Tramontano, A. 2006. The PMDB Protein Model Database Nuclei Acids Research, 34, 306-309

  105. Brenner, S., Tramontano, A. 2005. Sequences and topology: a decade of genomes, Curr. Opin. Struct. Biol., 15(3) 245-247.

  106. Raimondo, D., Giorgetti, A., Miele, AE., Tramontano, A. 2005. Evaluating the usefulness of protein structure models for molecular replacement, Bioinformatics, 21(S2) 72-76.

  107. Moult, J., Fidelis, K., Rost, B., and Hubbard, T. and Tramontano, A. 2005. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round VI, Proteins, S7, 3-7.

  108. Soro, S., Tramontano, A. 2005. Function Prediction at CASP6, Proteins, S7, 214-224.

  109. Book: Tramontano, A. 2005. The ten most wanted solutions in protein bioinformatics, Chapman&Hall/CRC Mathematical Biology and Medicine Series. 256 pp.

  110. Francisci, S., De Luca, C. Oliva, R., Morea, V., Tramontano, A. and Frontali, L., 2005. Aminoacylation and conformational properties of yeast mitochondrial mutants with respiratory deficiency, RNA, 11: 914-927.

  111. Cozzetto, D., Di Matteo, A. and Tramontano, A. 2005 Ten years of prediction ... and counting. FEBS Journal, 272, 881-882.

  112. Cozzetto, D., Tramontano, A. 2004 The relationship between multiple sequence alignment and the quality of protein comparative models. Proteins, 58, 151-157.

  113. Tramontano, A. 2004 Folding and sequence analysis. Encyclopedia of condensed matter physics, Elsevier Press, Elsevier, 2005.

  114. Tramontano, A. 2004 A brighter future for protein design. 2004. Angewandte Chemie, 116,2-3.

  115. Ghiotto, F., Fais, F., Valetto, A., Albesiano, E., Hashimoto, S., Dono, M., Ikematsu, H., Allen, S.L., Rai, K.R., Nardini, M., Tramontano, A., Ferrarini, M., Chiorazzi, N. 2004 Remarkably similar antigen receptors in a subset of patients with IgG+ chronic lymphocytic leukemia. Journal Clin, Inv. 113:1008-1016

  116. Tramontano, A., Morea,V. 2003 Assessment of homology based predictions in CASP 5. Proteins 52 (Suppl. 7) 352-368

  117. Travaglini-Allocatelli, C., Gianni, S., Morea, V., Tramontano, A., Soulimane, T. and Brunori, M. 2003 Exploring the cytochrome c folding: cyt c552 from Thermus Thermopilus folds through and on-pathway intermediate, J. Biol. Chem. 278(42) 41136-41140

  118. Tramontano, A. and Morea, V. 2003 Exploiting evolutionary relationships for predicting protein structures Biotechnology and Bioengeneering.

  119. Tramontano, A. 2003 Comparative modeling techniques: where are we? Comparative and Functional Genomics. 4:402-405

  120. Donini, M., Morea, V., Desiderio, A., Pashkoulov, D., Villani, M.E., Tramontano, A. and Benvenuto, E. 2003 Engineering stable cytoplasmic intrabodies with designed specificity. J. Mol. Biol. 330(2) 323-332

  121. Iliopolus,I., Tsoka, S., Andrade, M.,..., Tramontano, A.,...,Ouzounis, C. 2003 Evaluation of annotation strategies using an entire genome sequence. Bioinformatics, 19: 717-726

  122. Tramontano, A. 2003 La predizione della struttura tridimensionale delle proteine: una formidabile sfida per la biologia moderna Sapere, 3

  123. Tramontano, A. 2003 La Storia della Bioinformatica Enciclopedia Italiana in "Storia della Scienza", Istituto della Enciclopedia Italiana, 10v., 2001-2004, Vol. IX, 2003, 245-253

  124. Tramontano, A. 2003 Of men and machines Nat. Str. Biol. 10:87-90.

  125. Roccasecca, M., Ansuini H., Vitelli, A., Meola, A., Scarselli, E., Acali, S., Pezzanera, M., Bruni Ercole, B., McKeating, J., Yagnik, A., Lahm, A., Tramontano, A., Cortese, R., Nicosia, A. 2003. Binding of HCV E2 glycoprotein to CD81 is strain specific and is modulated by a complex interplay between hypervariable regions 1 and 2 J. Virol. 77:1856-1867.

  126. Lahm, A., A. Yagnik, A. Tramontano & U. Koch. 2002. Hepatitis C virus proteins as targets for drug development: the role of bioinformatics and modelling. Curr Drug Targets 3:(4): 281-96

  127. Tramontano, A., G. D'Alfonso & V. Morea. 2002. The challenge of protein structure prediction. Science Letters 25: 202-214.

  128. Book: Tramontano, A. 2002. Bioinformatica. Zanichelli, Bologna. 135 pp.

  129. Procopio, M., A. Lahm, A. Tramontano, L. Bonati & D. Pitea. 2002. A model for recognition of polychlorinated dibenzo-p-dioxins by the aryl hydrocarbon receptor. European Journal of Biochemistry 269: 13-8.

  130. Notomista, E., A. Lahm, A. Di Donato & A. Tramontano. 2003. Evolution of Bacterial and Archeal Multicomponent Monooxygenases. J. Mol. Evol. 56: 435-445.

  131. Moult, J., K. Fidelis, A. Zemla, T. Hubbard & A. Tramontano. 2002. The significance of performance ranking in CASP. Structure 10: 291-2.

  132. Cappello, V., A. Tramontano & U. Koch. 2002. Classification of proteins based on the properties of the ligand-binding site: the case of adenine-binding proteins. Proteins 47: 106-15.

  133. Tramontano, A., R. Leplae & V. Morea. 2001. Analysis and assessment of comparative modeling predictions in CASP4. Proteins Suppl 5: 22-38.

  134. Tramontano, A. 2001. Modelling of the NS3 Serine Protease of the Hepatitis C virus. In: R. Casadio & L. Masotti (ed.) Protein Sequence Analysis in the Post-Genomic Era, CLUEB, Bologna.

  135. Scognamiglio, R., E. Notomista, P. Barbieri, P. Pucci, F. Dal_Piaz, A. Tramontano & A. Di_Donato. 2001. Conformational analysis of putative regulatory subunit D of the toluene/o-xylene-monooxygenase complex from Pseudomonas stutzeri OX1. Protein Science : a Publication of the Protein Society 10: 482-90.

  136. Roccasecca, R., A. Folgori, B.B. Ercole, G. Puntoriero, A. Lahm, S. Zucchelli, R. Tafi, M. Pezzanera, G. Galfre, A. Tramontano, M.U. Mondelli, A. Pessi, A. Nicosia, R. Cortese & A. Meola. 2001. Mimotopes of the hyper variable region 1 of the hepatitis C virus induce cross-reactive antibodies directed against discontinuous epitopes. Molecular Immunology 38: 485-92.

  137. Roccasecca, R., A. Folgori, B.B. Ercole, G. Puntoriero, A. Lahm, S. Zucchelli, R. Tafi, M. Pezzanera, G. Galfre, A. Tramontano, M.U. Mondelli, A. Pessi, A. Nicosia, R. Cortese & A. Meola. 2001. Induction of cross-reactive humoral immune response by immunization with mimotopes of the hypervariable region 1 of the hepatitis C virus. International Reviews of Immunology 20: 289-300.

  138. Iliopoulos, I., S. Tsoka, M.A. Andrade, P. Janssen, B. Audit, A. Tramontano, A. Valencia, C. Leroy, C. Sander & C.A. Ouzounis. 2001. Genome sequences and great expectations. Genome Biol 2: on line.

  139. D'Alfonso, G., A. Tramontano & A. Lahm. 2001. Structural conservation in single-domain proteins: implications for homology modeling. Journal of Structural Biology 134: 246-56.


Last Updated ( Thursday, 26 May 2016 10:43 )