Anna Tramontano

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since 2001 Professor of Biochemistry,  University of Rome "La Sapienza"
2004 - 2010 Director of the Bioinformatics Program, CRS4, Pula (CA)
1996 - 2001 Director of the Computational Biology and Chemistry Department at  IRBM (Merck Research Laboratories in Pomezia, Rome)
Director of Information Technology and Research Information Systems at IRBM
Professor of Chimica Computazionale II at the University of Naples
in 1994/95 Director of Biocomputing Unit of IRBM
in 1990/93 Biocomputing Group Leader at  IRBM
Professor of Bioinformatics at the University of Milan
in 1988/90 Staff member of the European Laboratory for Molecular Biology in Heidelberg (D) in the Biocomputing Programme.
in 1987 Research fellow at International Institute of Genetics and Biophysics in Naples
in 1985/86 Consultant for Biosym Technologies Inc., San Diego, CA, USA
in 1984/85 Post-doctoral research fellow at the Department of Biochemistry and Biophysics of the University of California, San Francisco (USA)
in 1981/84 Research fellow at the International Institute of Genetics and Biophysics in Naples
in 1980 Laurea in Physics, summa cum laude, at the University of Naples


Teaching activities

  • Biofisica Computazionale, Corso di laurea in Fisica, Universita' "La Sapienza"
  • Biochimica II, Corso di laurea in Biotecnologie, Universita' "La Sapienza"
  • Biochimica I, Corso di laurea in Medicina e Chirugia, canale A, Universita' "La Sapienza"
  • Bioinformatica e Ingegneria proteica, corso di laurea in Biotecnologie mediche, Universita' "La Sapienza"
  • Bioinformatica e Proteomica, corso di laurea in Biotecnologie Farmaceutiche , Universita' "La Sapienza"

Past (very partial!)...

  • Biochimica, Master in Bioinformatica: Applicazioni Biomediche e Farmaceutiche, Universita' "La Sapienza"
  • Bioinformatica 2, Master in Bioinformatica: Applicazioni Biomediche e Farmaceutiche, Universita' "La Sapienza" 
  • Biochimica, Corso di laurea specialistica in Fisica
  • Biochimica, Corso di laurea in Fisica, Universita' "La Sapienza"
  • Structural Bioinformatics, NairobiStructural Bioinformatics, Pretoria
  • Structural Biology, Gulbenkian Institute
  • Biochimica 2, Master in Tecnologie Bioinformatiche applicate alla medicina personalizzata Consorzio21, Pula, Cagliari
  • Domini proteici, Corso di laurea in Biotecnologie, Universita' di Verona
  • The experimental interface, Master in Bioinformatics, University of Oxford, UK

Memberships and awards

Other activities (partal list)

  • Director: Master in Bioinformatica: Applicazioni biomediche e farmaceutiche (2002-2010)
  • Director: Master in Tecnologie Bioinformatiche applicate alla Medicina personalizzata, Consorzio21 Pula, Cagliari (2004-2005)
  • Organizer: EMBO Sectoral Meeting in Bioinformatics 2004
  • Organizer: Permanent European School in Bioinformatics
  • Organizer: 1st ESF training course on Molecular Interactions, Verona, Italy, 2002
  • Organizer: 2nd ESF training course on Molecular Interactions, Verona, Italy, 2002
  • Organiser: Third European Workshop in Drug Design, Siena, Italy, 2001
  • Organiser: Euroconference on Protein Folding and Structure Prediction, Torino, Italy, 1998
  • Organiser: Second European Workshop in Drug Design, Siena, Italy, 1998
  • Organiser: FEBS Practical Course Frontiers of Protein Structure Prediction, IRBM ,Rome, Italy, 1997
  • Organiser: EMBO Symposium on Structural Biology, EMBL, Heidelberg, Germany, 1997
  • Organiser: Practical Course Frontiers of Protein Structure Prediction, IRBM ,Rome, Italy 1995
  • Co-organiser: First European Workshop in Drug Design, Cortona, Italy, 1995

Invited to give seminars / lectures / conferences in

Argentina (Buenos Aires), Australia (Canberra, Lorne), Brasil (Rio de Janeiro), Canada (Québec), Croatia (Rovinj), Cuba (Havana), Denmark (Copenaghen), Finland (Turku, Tromso), France (Paris, Strasbourg), Germany (Munchen, Heidelberg, Braunschweig, Saarbrucken, Hamburg), Greece (Eraklion), India (Lucknow, Madurai), Israel (Eilat), Kenia (Nairobi), Mali (Bamako), Netherlands (Amsterdam, Njemegen), Norway (Oslo), Portugal (Oeiras), Russia (Moscow, Puschino), Saudi Arabia (Jeddah), South Africa (Pretoria),  Slovenia (Portoroz, Ljubjana), Spain (Madrid, Barcellona, La Coruna), Sweden (Stockholm, Uppsala), Switzerland (Ascona, Fribourg), Turkey (Istanbul, Antalya), UK (London., Oxford, Cambridge, Glasgow, Cardiff, Dover), USA (Asilomar, San Diego, Seattle, New York), Italy (all major cities).



Areas of research

  • Protein Structure Prediction
  • Protein structure analysis
  • Protein sequence analysis
  • Protein design
  • Antibody structure
  • Genome functional annotation
  • Viral proteins

(see also my ResearcherId page

  1.  Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T. and Tramontano, A. Critical Assessment of Methods of Protein Structure Prediction (CASP) – Progress and New directions in Round XI. In press
  2. Obarska-Kosinska, A., Iaconageli, A., Lepore, R. and Tramontano, A. PepComposer: computational design of peptides binding to a given protein surface, Nuclei Acids Research (2016) doi: 10.1093/nar/gkw366
  3. Leoni, G., Tramontano, A. A structural view of microRNA-target recognition, Nucleic Acids Research (2016) doi: 10.1093/nar/gkw043
  4. Milanetti, E., Raimondo,D., Tramontano, A. Prediction of the permeability of neutral drugs inferred from their solvation properties. Bioinformatics (2015) DOI: 10.1093/bioinformatics/btv725
  5. Monastyrskyy, B., D'Andrea, D., Fidelis, K., Tramontano, A. and Kryshtafovych, A. New encouraging developments in contact prediction: assessment of CASP11 results. Proteins (2015) doi: 10.1002/prot.24943
  6. Kryshtafovych, A, Barbato, A., Monastyrskyy, B., Fidelis, K., Schwede, T., Tramontano, A. Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11. Proteins (2015) doi: 10.1002/prot.24919
  7. Messih, M.A., Lepore, R., Tramontano, A. LoopIng: a template-based tool for predicting the structure of protein loops. Bioinformatics (2015) DOI: 10.1093/bioinformatics/btv438
  8. Iacoangeli, A., Marcatili, A. and Tramontano, A. Exploiting Homology Information in Non-template Based Prediction of Protein Structures. J. Chem. Theory Comput. (2015) 11 (10): 5045–5051 DOI: 10.1021/acs.jctc.5b00371
  9. Le Pera, L., Mazzapioda, M., Tramontano, A. 3USS: a web server for detecting alternative 3 ' UTRs from RNA-seq experiments (2015) Bioinformatics  31 (11): 1845-184 DOI: 10.1093/bioinformatics/btv035
  10. Di Marino, D., Bonome,E.L., Tramontano, A., Chinappi, M. All-Atom Molecular Dynamics Simulation of Protein Translocation through an alpha-Hemolysin Nanopore (2015) Journal of Physical Chemistry Letters 6 (15) : 2963-2968
  11. Di Marino, D., D'Annessa, I., Coletta, A., Via, A., Tramontano, A. Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: A computational study (2015) Proteins 83(3): 564-574 DOI: 10.1002/prot.24734
  12. Grassi L., Leoni, G. and Tramontano, A. RNA editing differently affects protein coding genes in D. melanogatsre and H. sapiens (2015) Science Reports (5) doi:10.1038/srep11550
  13. Dias R., Via A., Brandão MM., Tramontano A., Silva-Filho MC. Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in Lepidoptera. (2015) Insect Biochem Mol Biol.58:1-11. doi: 10.1016/j.ibmb.2014.12.009
  14. Domina, M., Lanza-Cariccio, V. Benfatto, S., D’Aliberti,D., Venza, Borgogni, M.E., Castellino, F., Biondo, C., D’Andrea, D., Grassi, L., Tramontano, A.,Teti, G., Felici, F. and Beninati, V. Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries. (2014) PLoS One, 9(12):e114159. DOI: 10.1371/journal.pone.0114159
  15. Tornatore, L;  Sandomenico, A; Raimondo, D; Low, C and Rocci, A and Tralau-Stewart, C and Capece, DD'Andrea, D; Bua, M; Boyle, E; van, Duin M; Zoppoli, P; Jaxa-Chamiec, A; Thotakura, AK;  Dyson, J; Walker, BA; Leonardi, A; Chambery, A; Driessen, C; Sonneveld, P; Morgan, G; Palumbo, A; Tramontano, A; Rahemtulla, A; Ruvo, M and Franzoso, G (2014) Cancer Cell 26: 495-508  DOI: 10.1016/j.ccr.2014.07.027
  16. Olimpieri, PP, Marcatili P, Tramontano A Tabhu: Tools for antibody humanization. (2015) Bioinformatics 31(3):434-5.  doi: 10.1093/bioinformatics/btu667
  17. Marcatili P, Olimpieri PP, Chailyan A, Tramontano A. Antibody structural modeling with PIGS. (2015) Nature Protocols. 9:2771–2783 DOI: 10.1038/nprot.2014.189
  18. Messih MA, Lepore R, Marcatili P, Tramontano A. Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chain of antibodies. (2014) Bioinformatics. doi:10.1093/bioinformatics/btu194
  19. Bonella, S.; Raimondo, D.; Milanetti, E, Tramontano, A., Ciccotti, G. Mapping the Hydropathy of Amino Acids Based on Their Local Solvation Structure Journal of Physical Chemistry B (2014) 118 (24):6604-6613 DOI: 10.1021/jp500980x>
  20. Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T. and Tramontano, A. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round X Proteins (2014) 82:1-6 
  21. Monastyrskyy, B., D'Andrea, D., Fidelis, K., Tramontano, A., Kryshtafovych, A. Evaluation of residue residue contact prediction in CASP10 Proteins (2014) 82:138-153
  22. Monastyrskyy, B., , Kryshtafovych, A., Moult, J., Tramontano. A., Fidelis K.,Assessment of protein disorder region predictions in CASP10 Proteins (2014) 82: 127-137
  23. Kryshtafovych, A., Barbato, A., Fidelis, K., Monastyrskyy, B., Schwede, T., Tramontano, A.,  Assessment of the assessment: evaluation of the model quality estimates in CASP10 Proteins (2014) 82: 112-126
  24. Olimpieri PP, Chailyan A, Tramontano A. Marcatili P Prediction of site-specific interactions in antibody antigen complexes: the proABC method and server. (2013) Bioinformatics 29(18): 2285-2291
  25. D'Andrea, D., Grassi, L., Mazzapioda, G. and Tramontano, A. FIDEA: a server for the functional interpretation of differential expression analysis Nucl. Acids Res. (1 July 2013) 41 (W1)
  26. Olimpieri, P.P., Chailyan, A., Tramontano, A. and Marcatili, P. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server (2013) Bioinformatics. 29(18):2285-91. doi: 10.1093/bioinformatics/btt369
  27. Lepore, R., Tramontano, A., Via, A. TiPs: A database of therapeutic targets in pathogens and associated tools Bioinformatics,(2013)  29(14):1821-2. doi: 10.1093/bioinformatics/btt289
  28. Marcatili, P. Ghiotto, F. Tenca, C., Chailyan, A., N. Mazzarello, AN., Yan X-J.,  Colombo, M., Albesiano, E., Bagnara, D., Cutrona, G., Morabito, F., Bruno, S., Ferrarini, M., Chiorazzi, N., Tramontano, A., Fais, F.Immunoglobulins expressed by chronic lymphocytic leukemia B cells show limited binding site structure variability (2013) J. Immun.,190(11):5771-8. doi: 10.4049/jimmunol.1300321
  29. Marcello, E. Saraceno, C. Musardo, S., Vara, H., de la Fuente, A.G.Pelucchi, S. Di Marino, D. Borroni, B., Tramontano, A., Pérez-Otaño, I., Padovani, A. Giustetto, M., Gardoni, F., Di Luca, M. Role of synaptic ADAM10 in plasticity and Alzheimer's disease (2013) J. Clin Inv., doi:10.1172/JCI65401
  30. Kosinski, J., Barbato, A., Tramontano, A. MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships (2013) Bioinformatics,29(7):953-4. doi: 10.1093/bioinformatics/btt062
  31. 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 (2013) BMC Genomics , 14:124. doi: 10.1186/1471-2164-14-124
  32. 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.
  33. Carbajo, D. and Tramontano, A. A resource for benchmarking the usefulness of protein structure models. BMC Bioinformatics (2012) 13:188.
  34. 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
  35. Barbato, A., Benkert, P., Schwede, T., Tramontano, A., Kosinski J. Improving your target-template alignment with MODalign. (2012) Bioinformatics, doi: 10.1093/bioinformatics/bts070
  36. Chailyan, A., Tramontano, A., Marcatili, P. A database of immunogloblins with integrated tools: DIGIT Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr806
  37. 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. 417(1):576-581
  38. Raimondo D., Romano V., Calvanese L., Gabriella D’Auria G., Tramontano A. and Falcigno l.(21012) Toward a better understanding of the interaction between TGF-b family members and their ALK receptors J. Mol. Model. 18 (8), 3617-362
  39. 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.
  40. Grassi L., Tramontano, A. (2011) Horizontal and vertical growth of S. cerevisiae metabolic network. BMC Evolutionary Biology, 11:301
  41. Moult, J., Fidelis, K., Kryshtafovych, A. and Tramontano, A. (2011) Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round IX. Proteins,  79,  S10: 1–5
  42. Monastyrskyy, B.,  Fidelis, K.,  Moult, J.,  Tramontano, A. and  Kryshtafovych, A. (2011) Evaluation of model quality predictions in CASP9, Proteins, 79,  S10: 91–106
  43. Lepore A, 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 doi:10.1016/j.bbrc.2011.12.009
  44. 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.
  45. Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JAM, Tramontano A, Schneider MV (2011) 10 simple rules for developing a short bioinformatics training course. PLoS Computational Biology. 7(10): e1002245. doi:10.1371/journal.pcbi.1002245
  46. 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, Molecular Medicine, 17:1188-1195
  47. Kryshtafovych, A.,   Fidelis, K. and Tramontano, A. (2011) Evaluation of residue-residue contacts predictions in CASP9, Proteins, 79,  S10:119–125
  48. Monastyrskyy, B.,   Fidelis, K.,   Moult, J.,   Tramontano, A. and  Kryshtafovych, A. (2011) Evaluation of disorder prediction in CASP9, Proteins, 79,  S10:107–118
  49. 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.
  50. Chailyan, A., Marcatili, P., Tramontano, A. The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. The FEBS Journal, DOI: 10.1111/j.1742-4658.2011.08207.x
  51. 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
  52. Floris, M., Raimondo, D., Leoni, G., Orsini, M., Marcaili, P. amd Tramontano, A.(2011) MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics, 79(5) 1513–1524
  53. 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
  54. 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 Biology, BMC Evolutionary Biology11:72doi:10.1186/1471-2148-11-72
  55. Chailyan, A., Marcatili, P., Cirillo, D. Tramontano, A. (2011) Structural repertoire of immunoglobulin λ light chains. Proteins, 79(5):1513-24
  56. Leoni, G., Le Pera, L., Ferre', F., Raimondo, D., Tramontano, A. 2011 Coding potential of the products of alternative splicing in human. Genome Biology 12:R9 doi:10.1186/gb-2011-12-1-r9
  57. 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.001406
  58. 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, Database issue. 39:d268-d271
  59. Le Pera, L., Marcatili, P., Tramontano, A. Picmi: mapping point mutations on genomes (2010) Bioinformatics, 26(22): 2904-2905
  60. 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
  61. 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
  62. 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
  63. Tramontano, A Bioinformatics. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. (2009) DOI: 10.1002/9780470015902.a0001900.pub2
  64. Tramontano, A. No protein is an island. Current Opin. Struct. Biol. (2009) 19(3): 310-311 
  65. Moult, J., Fidelis, K., Kryshtafovych, A., Rost, B. and Tramontano, A. Critical Assessment of Protein Structure Prediction (CASP) - Round VIII. (2009) Proteins, 77: 1-4
  66. Cozzetto, D., Kryshtafovych, A. and Tramontano, A. Evaluation of CASP8 Model Quality Predictions. (2009) Proteins 77: 157-166
  67. Cozzetto, D., Kryshtafovych, A., Fidelis, K., Moult, J., Rost, B. and Tramontano, A. Evaluation of template-based models in CASP8 with standard measures. (2009) Proteins,11:18-28
  68. 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 .
  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. Tramontano, A., Jones, D., Rychlewski, L.,  Casadio, R. Martelli, P.,  Raimondo, D. and  Giorgetti, A.  (2008) In Frishman, D. and Valencia, A. (eds.), Modern genome annotation: the BioSapiens network. Springer. ISBN: 978-3-211-75122-0
  71. Marcatili, P., Rosi, A. and Tramontano, A. PIGS: Automatic prediction of antibody structures (2008) Bioinformatics, 24(17):1953-1954.
  72. 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
  73. 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.
  74. 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.
  75. 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
  76. Marcatili, P., Bussotti, G., Tramontano, A. The MoVin server (2008) BMC Bioinformatics, 9:S11
  77. 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.
  78. Cozzetto, D., Giorgetti, A., Raimondo, D. and Tramontano, A. The evaluation of protein structure prediction results. (2008) Molecular Biotechnology 39: 1-8
  79. 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
  80. Tramontano, A. and Pearson, W.R. The completeness of biological space (2007) Curr. Op. Struct. Biol. 17:334-336
  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. Protein Structure Prediction: Concepts and applications Wiley-VCH, Wenheim  (2006).
  94. Book: Tramontano, A. Introduction to Bioinformatics CRC Press, New York (2006).
  95. 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.
  96. 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.
  97. 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.
  98. Pellegrini Calace, M., Soro, S. and Tramontano, A. Revisiting the prediction of protein function at CASP6 FEBS J. (2006) 273, 2977-2983.
  99. 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.
  100. Tramontano, A. The role of molecular modelling in biomedical research (2006) FEBS Lett., 580 (12), 2928-2934.
  101. 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
  102. 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.
  103. Book: Tramontano, A. 2006. Protein Structure Prediction, Wiley Inc. Weinheim, Germany.
  104. Tramontano, A. Bioinformatica, XXI Secolo - Aggiornamento dell'Enciclopedia italiana di scienze, lettere ed arti, Treccani, 2006 .
  105. 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
  106. Brenner, S., Tramontano, A. 2005. Sequences and topology: a decade of genomes, Curr. Opin. Struct. Biol., 15(3) 245-247.
  107.  Raimondo, D., Giorgetti, A., Miele, AE., Tramontano, A. 2005. Evaluating the usefulness of protein structure models for molecular replacement, Bioinformatics, 21(S2) 72-76.
  108. 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.
  109. Soro, S., Tramontano, A. 2005. Function Prediction at CASP6, Proteins, S7, 214-224.
  110. Book: Tramontano, A. 2005. The ten most wanted solutions in protein bioinformatics, Chapman&Hall/CRC Mathematical Biology and Medicine Series. 256 pp.
  111. 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.
  112. Cozzetto, D., Di Matteo, A. and Tramontano, A. 2005 Ten years of prediction ... and counting. FEBS Journal, 272, 881-882.
  113. Cozzetto, D., Tramontano, A. 2004 The relationship between multiple sequence alignment and the quality of protein comparative models. Proteins, 58, 151-157.
  114. Tramontano, A. 2004 Folding and sequence analysis. Encyclopedia of condensed matter physics, Elsevier Press, Elsevier, 2005.
  115. Tramontano, A. 2004 A brighter future for protein design. 2004. Angewandte Chemie, 116,2-3.
  116. 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
  117. Tramontano, A., Morea,V. 2003 Assessment of homology based predictions in CASP 5. Proteins 52 (Suppl. 7) 352-368
  118. 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
  119. Tramontano, A. and Morea, V. 2003 Exploiting evolutionary relationships for predicting protein structures Biotechnology and Bioengeneering.
  120. Tramontano, A. 2003 Comparative modeling techniques: where are we? Comparative and Functional Genomics. 4:402-405
  121. 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
  122. Iliopolus,I., Tsoka, S., Andrade, M.,..., Tramontano, A.,...,Ouzounis, C. 2003 Evaluation of annotation strategies using an entire genome sequence. Bioinformatics, 19: 717-726
  123. Tramontano, A. 2003 La predizione della struttura tridimensionale delle proteine: una formidabile sfida per la biologia moderna Sapere,3
  124. 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
  125. Tramontano, A. 2003 Of men and machines Nat. Str. Biol. 10:87-90.
  126. 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.
  127. 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
  128. Tramontano, A., G. D'Alfonso & V. Morea. 2002. The challenge of protein structure prediction. Science Letters 25: 202-214.
  129. Book: Tramontano, A. 2002. Bioinformatica. Zanichelli, Bologna. 135 pp.
  130. 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.
  131. Notomista, E., A. Lahm, A. Di Donato & A. Tramontano. 2003. Evolution of Bacterial and Archeal Multicomponent Monooxygenases. J. Mol. Evol. 56: 435-445.
  132. Moult, J., K. Fidelis, A. Zemla, T. Hubbard & A. Tramontano. 2002. The significance of performance ranking in CASP. Structure 10: 291-2.
  133. 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.
  134. Tramontano, A., R. Leplae & V. Morea. 2001. Analysis and assessment of comparative modeling predictions in CASP4. Proteins Suppl 5: 22-38.
  135. 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.
  136. 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.
  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. 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.
  138. 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.
  139. 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.
  140. 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.
  141. Morea, V., A.M. Lesk & A. Tramontano. 2000. Antibody modeling: implications for engineering and design. Methods (San Diego, Calif.) 20: 267-79.
  142. Yagnik, A.T., A. Lahm, A. Meola, R.M. Roccasecca, B.B. Ercole, A. Nicosia & A. Tramontano. 2000. A model for the hepatitis C virus envelope glycoprotein E2. Proteins 40: 355-66.
  143. Tramontano, A. & F. Felici. 2000. Exploring molecular recognition by combinatorial and rational approaches. In: L. Alberghina (ed.) Protein Engineering for Industrial Biotechnology, GORDON & BREACH SCIENTIFIC PUB, New York
  144. Tamames, J. & A. Tramontano. 2000. DANTE: a workbench for sequence analysis. Trends in Biochemical Sciences 25: 402-3.
  145. Santi, E., S. Capone, C. Mennuni, A. Lahm, A. Tramontano, A. Luzzago & A. Nicosia. 2000. Bacteriophage lambda display of complex cDNA libraries: a new approach to functional genomics. Journal of Molecular Biology 296: 497-508.
  146. Pacini, L., A. Vitelli, G. Filocamo, L. Bartholomew, M. Brunetti, A. Tramontano, C. Steinkuhler & G. Migliaccio. 2000. In vivo selection of protease cleavage sites by using chimeric Sindbis virus libraries. Journal of Virology 74: 10563-70.
  147. Coscia, M.R., V. Morea, A. Tramontano & U. Oreste. 2000. Analysis of a cDNA sequence encoding the immunoglobulin heavy chain of the Antarctic teleost Trematomus bernacchii. Fish Shellfish Immunol 10: 343-57.
  148. Filocamo, G., L. Pacini, C. Nardi, L. Bartholomew, M. Scaturro, P. Delmastro, A. Tramontano, R. De_Francesco & G. Migliaccio. 1999. Selection of functional variants of the NS3-NS4A protease of hepatitis C virus by using chimeric sindbis viruses. Journal of Virology 73: 561-75.
  149. Al-Lazikani, B., C. Chothia, A.M. Lesk, V. Morea, M. Rustici & A. Tramontano. 1999. Immunoglobulin Structure. In: T.E. Creighton (ed.) Encyclopedia of Molecular Biology, John Wiley and Sons, NY.
  150. Leplae, R., T. Hubbard & A. Tramontano. 1998. GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency. Proteins 30: 339-51.
  151. Tramontano, A. 1998. Homology modeling with low sequence identity. Methods (San Diego, Calif.) 14: 293-300.
  152. Puntoriero, G., A. Meola, A. Lahm, S. Zucchelli, B.B. Ercole, R. Tafi, M. Pezzanera, M.U. Mondelli, R. Cortese, A. Tramontano, G. Galfre_ & A. Nicosia. 1998. Towards a solution for hepatitis C virus hypervariability: mimotopes of the hypervariable region 1 can induce antibodies cross-reacting with a large number of viral variants. The Embo Journal 17: 3521-33.
  153. Pasquo, A., M.C. Nardi, N. Dimasi, L. Tomei, C. Steinkuhler, P. Delmastro, A. Tramontano & R. De_Francesco. 1998. Rational design and functional expression of a constitutively active single-chain NS4A-NS3 proteinase. Folding & Design 3: 433-41.
  154. Morea, V., A. Tramontano, M. Rustici, C. Chothia & A.M. Lesk. 1998. Conformations of the third hypervariable region in the VH domain of immunoglobulins. Journal of Molecular Biology 275: 269-94.
  155. Morea, V., R. Leplae & A. Tramontano. 1998. Protein structure prediction and design. Biotechnol Annu Rev 4: 177-214.
  156. Lo Bello, M., M. Nuccetelli, E. Chiessi, A. Lahm, A.P. Mazzetti, A. Battistoni, A.M. Caccuri, A.J. Oakley, M.W. Parker, A. Tramontano, G. Federici & G. Ricci. 1998. Mutations of Gly to Ala in human glutathione transferase P1-1 affect helix 2 (G-site) and induce positive cooperativity in the binding of glutathione. Journal of Molecular Biology 284: 1717-25.
  157. Amati, V. & A. Tramontano. 1997. Modelling of the NS3 protease of hepatitis C virus: implications for the prediction of the structure of related enzymes. Current topics in Peptide & Protein Research 2: 153-158.
  158. Zappacosta, F., P. Ingallinella, A. Scaloni, A. Pessi, E. Bianchi, M. Sollazzo, A. Tramontano, G. Marino & P. Pucci. 1997. Surface topology of Minibody by selective chemical modifications and mass spectrometry. Protein Science : a Publication of the Protein Society 6: 1901-9.
  159. Urbani, A., E. Bianchi, F. Narjes, A. Tramontano, R. De_Francesco, C. Steinkuhler & A. Pessi. 1997. Substrate specificity of the hepatitis C virus serine protease NS3. The Journal of Biological Chemistry 272: 9204-9.
  160. Neddermann, P., L. Tomei, C. Steinkuhler, P. Gallinari, A. Tramontano & R. De_Francesco. 1997. The nonstructural proteins of the hepatitis C virus: structure and functions. Biological Chemistry 378: 469-76.
  161. Morea, V., A. Tramontano, M. Rustici, C. Chothia & A.M. Lesk. 1997. Antibody structure, prediction and redesign. Biophysical Chemistry 68: 9-16.
  162. Zappacosta, F., A. Pessi, E. Bianchi, S. Venturini, M. Sollazzo, A. Tramontano, G. Marino & P. Pucci. 1996. Probing the tertiary structure of proteins by limited proteolysis and mass spectrometry: the case of Minibody. Protein Science : a Publication of the Protein Society 5: 802-13.
  163. Hubbard, T.J., A.M. Lesk & A. Tramontano. 1996. Gathering them in to the fold. Nature Structural Biology 3: 313.
  164. Hubbard, T. & A. Tramontano. 1996. Update on protein structure prediction: results of the 1995 IRBM workshop. Folding & Design 1: R55-63.
  165. Hubbard, T., J. Park, A. Lahm, R. Leplae & A. Tramontano. 1996. Protein structure prediction: playing the fold. Trends in Biochemical Sciences 21: 279-81.
  166. Failla, C.M., E. Pizzi, R. De_Francesco & A. Tramontano. 1996. Redesigning the substrate specificity of the hepatitis C virus NS3 protease. Folding & Design 1: 35-42.
  167. De Francesco, R., A.N. Urbani, M. Tomei, C. L. Steinkuhler & A. Tramontano. 1996. A zinc binding site in viral serine proteinases. Biochemistry 36: 13282-13287.
  168. Pizzi, E., R. Cortese & A. Tramontano. 1995. Mapping epitopes on protein surfaces. Biopolymers 36: 675-80.
  169. Amati, V., T.M. Werge, A. Cattaneo & A. Tramontano. 1995. Identifying a putative common binding site shared by substance P receptor and an anti-substance P monoclonal antibody. Protein Engineering 8: 403-8.
  170. Ammendola, S., G. Raucci, O. Incani, A. Mele, A. Tramontano & A. Wallace. 1995. Replacing the glutamate ligand in the structural zinc site of Sulfolobus solfataricus alcohol dehydrogenase with a cysteine decreases thermostability. Protein Engineering 8: 31-7.
  171. Cortese, R., P. Monaci, A. Nicosia, A. Luzzago, F. Felici, G. Galfre, A. Pessi, A. Tramontano & M. Sollazzo. 1995. Identification of biologically active peptides using random libraries displayed on phage. Current Opinion in Biotechnology 6: 73-80.
  172. Helmer_Citterich, M., E. Rovida, A. Luzzago & A. Tramontano. 1995. Modelling antibody-antigen interactions: ferritin as a case study. Molecular Immunology 32: 1001-10.
  173. Leplae, R., A. Lahm & A. Tramontano. 1995. Protein structural analysis as a tool for protein design. Biopolymers 37: 377-382.
  174. Leplae, R. & A. Tramontano. 1995. PLANET: a phage library analysis expert tool. Physiological Chemistry and Physics and Medical Nmr 27: 331-8.
  175. Tramontano, A. 1995. The archtecture of loops in proteins. pp. 239-259. In: H.O. Villar (ed.) Advances in Computational Biology, JAI Press, Greenwich.
  176. Tramontano, A. 1995. Gli universi delle proteine. BioIt II: 33-35.
  177. Tramontano, A. & R. Cortese. 1995. Gli elementi architettonici delle proteine: le strutture beta. FORME 5: 9-12.
  178. Tramontano, A. & R. Cortese. 1995. Gli elementi architettonici delle proteine: i super-folds. FORME 6: 11-14.
  179. Tramontano, A. & R. Cortese. 1995. Gli elementi architettonici delle proteine: la loro predizione. FORME 6: 19-21.
  180. Tramontano, A. & R. Cortese. 1995. Gli elementi architettonici delle proteine: i loops. FORME 6: 5-7.
  181. Tramontano, A., A. Pessi, A. Lahm & R. Cortese. 1995. Gli elementi architettonici delle proteine: l'elica anfipatica. FORME 4: 3-6.
  182. Lotti, M., A. Tramontano, S. Longhi, F. Fusetti, S. Brocca, E. Pizzi & L. Alberghina. 1994. Variability within the Candida rugosa lipases family. Protein Engineering 7: 531-5.
  183. Tramontano, A., E. Bianchi, S. Venturini, F. Martin, A. Pessi & M. Sollazzo. 1994. The making of the minibody: an engineered beta-protein for the display of conformationally constrained peptides. Journal of Molecular Recognition : Jmr 7: 9-24.
  184. Pizzi, E., A. Tramontano, L. Tomei, N. La_Monica, C. Failla, M. Sardana, T. Wood & R. De_Francesco. 1994. Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. Proceedings of the National Academy of Sciences of the United States of America 91: 888-92.
  185. Pizzi, E., M. Helmer-Citterich & A. Tramontano. 1994. Structural and Dynamic Models of biomedical interest. In: A. Colosimo (ed.) Structural and Dynamic Models of biomedical interest, C.I.S.B., Rome.
  186. Orlandini, M., A. Santucci, A. Tramontano, P. Neri & S. Oliviero. 1994. Cloning, characterization, and modeling of a monoclonal anti-human transferrin antibody that competes with the transferrin receptor. Protein Science : a Publication of the Protein Society 3: 1476-84.
  187. Helmer_Citterich, M. & A. Tramontano. 1994. PUZZLE: a new method for automated protein docking based on surface shape complementarity. Journal of Molecular Biology 235: 1021-31.
  188. Bianchi, E., S. Venturini, A. Pessi, A. Tramontano & M. Sollazzo. 1994. High level expression and rational mutagenesis of a designed protein, the minibody. From an insoluble to a soluble molecule. Journal of Molecular Biology 236: 649-59.
  189. Pessi, A., E. Bianchi, A. Crameri, S. Venturini, A. Tramontano & M. Sollazzo. 1993. A designed metal-binding protein with a novel fold. Nature 362: 367-9.
  190. Tramontano, A., E. Pizzi, F. Felici, A. Luzzago, A. Nicosia & R. Cortese. 1993. A database system for handling phage library-derived sequences. Gene 128: 143-4.
  191. Tramontano, A. & A.M. Lesk. 1993. La conformazione delle anse nelle proteine globulari. Biotec 4: 19-23.
  192. Savino, R., A. Lahm, M. Giorgio, A. Cabibbo, A. Tramontano & G. Ciliberto. 1993. Saturation mutagenesis of the human interleukin 6 receptor-binding site: implications for its three-dimensional structure. Proceedings of the National Academy of Sciences of the United States of America 90: 4067-71.
  193. Bianchi, E., M. Sollazzo, A. Tramontano & A. Pessi. 1993. Chemical synthesis of a designed beta-protein through the flow-polyamide method. International Journal of Peptide and Protein Research 41: 385-93.
  194. Luzzago, A., F. Felici, A. Tramontano, A. Pessi & R. Cortese. 1993. Mimicking of discontinuous epitopes by phage-displayed peptides, I. Epitope mapping of human H ferritin using a phage library of constrained peptides. Gene 128: 51-7.
  195. Luzzago, A., F. Felici, A. Tramontano & R. Cortese. 1993. In vitro selection of peptides from molecular repertoires. Rend. Fis. Acc. Lincei 9: 359-366.
  196. Lotti, M., R. Grandori, F. Fusetti, S. Longhi, S. Brocca, A. Tramontano & L. Alberghina. 1993. Cloning and analysis of Candida cylindracea lipase sequences. Gene 124: 45-55.
  197. Lesk, A.M. & A. Tramontano. 1993. An atlas of antibody combining sites. In: M.H.V. Van Regenmortel (ed.) Structure of antigens, CRC Press, New York.
  198. Bianchi, E., M. Sollazzo, A. Tramontano & A. Pessi. 1993. Affinity purification of a difficult-sequence protein. Implications for the inclusion of capping in synthetic protocols. International Journal of Peptide and Protein Research 42: 93-6.
  199. Tramontano, A. & A.M. Lesk. 1992. Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations. Proteins 13: 231-45.
  200. Sander, C., G. Vriend, F. Bazan, A. Horovitz, H. Nakamura, L. Ribas, A.V. Finkelstein, A. Lockhart, R. Merkl & A. Tramontano. 1992. Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins 12: 105-10.
  201. Longhi, S., M. Lotti, F. Fusetti, E. Pizzi, A. Tramontano & L. Alberghina. 1992. Homology-derived three-dimensional structure prediction of Candida cylindracea lipase. Biochimica Et Biophysica Acta 1165: 129-33.
  202. Lesk, A.M. & A. Tramontano. 1992. Computational analysis of protein structures: ponder the known, model the unknown. Binary 4: 15-16.
  203. Rosati, M., M. Marino, A. Franze, A. Tramontano & G. Grimaldi. 1991. Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic Acids Research (Online) 19: 5661-7.
  204. Cosmi, C., Macchiato, M.F., Tramontano, A. 1991.A method to evaluate the relative weights of structural and functional constraints on a genome.Il Nuovo Cimento 13:553-563
  205. Tramontano, A. & A.M. Lesk. 1990. Antibody structure and structural predictions useful in guiding antibody engineering Antibody engineering, Freeman and Co., NY.
  206. Tramontano, A., C. Chothia & A.M. Lesk. 1990. Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins. Journal of Molecular Biology 215: 175-82.
  207. Sollazzo, M., D. Castiglia, R. Billetta, A. Tramontano & M. Zanetti. 1990. Structural definition by antibody engineering of an idiotypic determinant. Protein Engineering 3: 531-9.
  208. Macchiato, M.F. & A. Tramontano. 1990. VARIANT: a store and retrieval system for human haemoglobin variants. Computer Methods and Programs in Biomedicine 31: 113-4.
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  224. Cuomo, V.M., M.F. and Tramontano, A. 1983. Thermodynamic characteristics of a biological organism: information value of a gene and a protein as a measure of the efficiency and as index of selective pressure. Il Nuovo Cimento 2: 1582-1601.

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