A database of immunoglobulins with integrated tools: DIGIT

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Chailyan, Anna ^a   Tramontano, Anna ^a,b   Marcatili, Paolo ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; IMMUNOGLOBULIN; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN LIGHT CHAIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPLEMENTARITY DETERMINING REGION; DATA ANALYSIS; DATA BASE; DATABASE OF IMMUNOGLOBULINS WITH INTEGRATED TOOLS; GERM LINE; IMMUNOGLOBULIN VARIABLE REGION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MUTATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

DATABASES, PROTEIN; IMMUNOGLOBULIN VARIABLE REGION; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS; SOFTWARE; SYSTEMS INTEGRATION; TERMINOLOGY AS TOPIC;

EID: 84859572771     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr806     Document Type: Article

References (22)

1. Johnson,G. and Wu,T.T. (2001) Kabat Database and its applications: future directions. Nucleic Acids Res., 29, 205-206. (Pubitemid 32054448)
2. Martin,C.R. (2010) Protein Sequence and Structure Analysis of Antibody Variable Domains. Springer, New York.
3. Retter,I., Althaus,H.H., Munch,R. and Muller,W. (2005) VBASE2, an integrative V gene database. Nucleic Acids Res., 33, D671-674. (Pubitemid 40207959)
4. Giudicelli,V., Duroux,P., Ginestoux,C., Folch,G., Jabado-Michaloud,J., Chaume,D. and Lefranc,M.P. (2006) IMGT/ LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res., 34, D781-784.
5. 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, 323-332. (Pubitemid 36773705)
6. Ghiotto,F., Fais,F., Valetto,A., Albesiano,E., Hashimoto,S., Dono,M., Ikematsu,H., Allen,S.L., Kolitz,J., Rai,K.R. et al. (2004) Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia. J. Clin. Invest., 113, 1008-1016. (Pubitemid 38544122)
7. Ghiotto,F., Marcatili,P., Tenca,C., Calevo,M.G., Yan,X.J., Albesiano,E., Bagnara,D., Colombo,M., Cutrona,G., Chu,C.C. et al. (2011) Mutation pattern of paired immunoglobulin heavy and light variable domains in chronic lymphocytic leukemia B-cells. Mol. Med., in press; doi:10.2119/molmed.2011.00104.
8. Sollazzo,M., Castiglia,D., Billetta,R., Tramontano,A. and Zanetti,M. (1990) Structural definition by antibody engineering of an idiotypic determinant. Protein Eng., 3, 531-539. (Pubitemid 20290030)
9. Zibellini,S., Capello,D., Forconi,F., Marcatili,P., Rossi,D., Rattotti,S., Franceschetti,S., Sozzi,E., Cencini,E., Marasca,R. et al. (2011) Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma. Haematologica, 95, 1792-1796.
10. Chailyan,A., Marcatili,P., Cirillo,D. and Tramontano,A. (2010) Structural repertoire of immunoglobulin lambda light chains. Proteins, 79, 1513-1524.
11. Chailyan,A., Marcatili,P. and Tramontano,A. (2010) The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. FEBS J., 278, 2858-2866.
12. Chothia,C., Lesk,A.M., Tramontano,A., Levitt,M., Smith-Gill,S.J., Air,G., Sheriff,S., Padlan,E.A., Davies,D., Tulip,W.R. et al. (1989) Conformations of immunoglobulin hypervariable regions. Nature, 342, 877-883. (Pubitemid 20021331)
13. Helmer-Citterich,M., Rovida,E., Luzzago,A. and Tramontano,A. (1995) Modelling antibody-antigen interactions: ferritin as a case study. Mol. Immunol., 32, 1001-1010.
14. Marcatili,P., Rosi,A. and Tramontano,A. (2008) PIGS: automatic prediction of antibody structures. Bioinformatics, 24, 1953-1954.
15. Morea,V., Lesk,A.M. and Tramontano,A. (2000) Antibody modeling: implications for engineering and design. Methods, 20, 267-279. (Pubitemid 32905162)
16. Morea,V., Tramontano,A., Rustici,M., Chothia,C. and Lesk,A.M. (1997) Antibody structure, prediction and redesign. Biophys Chem., 68, 9-16. (Pubitemid 28064649)
17. Morea,V., Tramontano,A., Rustici,M., Chothia,C. and Lesk,A.M. (1998) Conformations of the third hypervariable region in the VH domain of immunoglobulins. J. Mol. Biol., 275, 269-294. (Pubitemid 28030004)
18. Tramontano,A., Chothia,C. and Lesk,A.M. (1990) Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins. J. Mol. Biol., 215, 175-182. (Pubitemid 20301312)
19. Tramontano,A. and Lesk,A.M. (1992) Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations. Proteins, 13, 231-245.
20. Al-Lazikani,B., Lesk,A.M. and Chothia,C. (1997) Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol., 273, 927-948. (Pubitemid 27493729)
21. Chothia,C. and Lesk,A.M. (1987) Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol., 196, 901-917. (Pubitemid 17127946)
22. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2009) GenBank. Nucleic Acids Res., 37, D26-D31.