SAbDab: The structural antibody database

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Dunbar, James ^a   Krawczyk, Konrad ^a   Leem, Jinwoo ^a   Baker, Terry ^b   Fuchs, Angelika ^c   Georges, Guy ^c   Shi, Jiye ^b   Deane, Charlotte M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UCB PHARMA   (Belgium)

^c ROCHE INNOVATION CENTER MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANTIBODY STRUCTURE; ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPLEMENTARITY DETERMINING REGION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN DOMAIN; ANTIGEN ANTIBODY COMPLEX; COMPUTER INTERFACE; CONFORMATION; DATA PROCESSING; FACTUAL DATABASE; HEAVY CHAIN; LIGHT CHAIN; STRUCTURAL ANTIBODY DATABASE; ANTIBODY AFFINITY; ANTIBODY COMBINING SITE; CHEMISTRY; GENETICS; INTERNET; NOMENCLATURE;

ANTIBODY; COMPLEMENTARITY DETERMINING REGION;

ANTIBODIES; ANTIBODY AFFINITY; BINDING SITES, ANTIBODY; COMPLEMENTARITY DETERMINING REGIONS; DATABASES, PROTEIN; INTERNET; PROTEIN CONFORMATION; TERMINOLOGY AS TOPIC;

EID: 84891771647     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1043     Document Type: Article

References (38)

1. Walsh, G. (2010) Biopharmaceutical benchmarks 2010. Nat. Biotechnol., 28, 917-924.
2. Kuroda, D., Shirai, H., Jacobson, M.P. and Nakamura, H. (2012) Computer-aided antibody design. Protein Eng. Des. Sel., 25, 507-522.
3. Choi, Y. and Deane, C.M. (2011) Predicting antibody complementarity determining region structures without classification. Mol. BioSyst., 7, 3327-3334.
4. Krawczyk, K., Baker, T., Shi, J. and Deane, C.M. (2013) Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking. Protein Eng. Des. Sel., 26, 621-629.
5. Epp, O., Lattman, E.E., Schiffer, M., Huber, R. and Palm, W. (1975) The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-A resolution. Biochemistry, 14, 4943-4952.
6. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
7. Johnson, G. and Wu, T.T. (2001) Kabat Database and its applications: future directions. Nucleic Acids Res., 29, 205-206.
8. Retter, I., Althaus, H.H., Munch, R. and Muller, W. (2005) VBASE2, an integrative V gene database. Nucleic Acids Res., 33, D671-D674.
9. Lefranc, M.P., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G., Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J. et al. (2009) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res., 37, D1006-D1012.
10. Martin, A.C.R. (2010) Antibody Engineering, Vol. 2. Protein Se. Springer, Berlin Heidelberg, pp. 33-51.
11. Ansari, H.R., Flower, D.R. and Raghava, G.P.S. (2010) AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res., 38, D847-D853.
12. Ponomarenko, J., Papangelopoulos, N., Zajonc, D.M., Peters, B., Sette, A. and Bourne, P.E. (2011) IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res., 39, D1164-D1170.
13. Chailyan, A., Tramontano, A. and Marcatili, P. (2012) A database of immunoglobulins with integrated tools: DIGIT. Nucleic Acids Res., 40, D1230-D1234.
14. Chothia, C., Lesk, A., 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.
15. Dunbar, J., Fuchs, A., Shi, J. and Deane, C.M. (2013) ABangle: characterising the VH-VL orientation in antibodies. Protein Eng. Des. Sel., 26, 611-620.
16. Chothia, C. and Lesk, A.M. (1987) Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol., 196, 901-917.
17. Morea, V., Tramontano, A., Rustici, M., Chothia, C., Lesk, A.M., Angeletti, M.P. and Roma, P. (1998) Conformations of the third hypervariable region in the VH domain of immunoglobulins. J. Mol. Biol., 275, 269-294.
18. Abhinandan, K.R. and Martin, A.C.R. (2008) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol. Immunol., 45, 3832-3839.
19. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
20. Weichenberger, C.X., Pozharski, E. and Rupp, B. (2013) Visualizing ligand molecules in twilight electron density. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 69, 195-200.
21. Wang, R., Fang, X., Lu, Y., Yang, C.Y. and Wang, S. (2005) The PDBbind database: methodologies and updates. J. Med. Chem., 48, 4111-4119.
22. Kastritis, P.L., Moal, I.H., Hwang, H., Weng, Z., Bates, P.A., Bonvin, A.M.J.J. and Janin, J. (2011) A structure-based benchmark for protein-protein binding affinity. Protein Sci., 20, 482-491.
23. Wu, T. and Kabat, E. (1970) An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med., 132, 211-250.
24. MacCallum, R.M., Martin, A.C.R. and Thornton, J.M. (1996) Antibody-antigen interactions: contact analysis and binding site topography. J. Mol. Biol., 262, 732-745.
25. Lefranc, M.P., Pommie, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc, G. (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol., 27, 55-77.
26. Al-Lazikani, B., Lesk, A. and Chothia, C. (1997) Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol., 273, 927-948.
27. North, B., Lehmann, A. and Dunbrack, R.L. (2011) A new clustering of antibody CDR loop conformations. J. Mol. Biol., 406, 228-256.
28. Lara-Ochoa, F., Almagro, J.C., Vargas-Madrazo, E. and Conrad, M. (1996) Antibody-antigen recognition: a canonical structure paradigm. J. Mol. Evol., 43, 678-84.
29. Martin, A.C.R. and Thornton, J.M. (1996) Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. J. Mol. Biol., 263, 800-815.
30. Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M. and Hornik, K. (2013) Cluster: cluster analysis basics and extensions, R package version 1.14.4.
31. Riechmann, L., Clark, M., Waldmann, H. and Winter, G. (1988) Reshaping human antibodies for therapy. Nature, 332, 323-327.
32. Foote, J. and Winter, G. (1992) Antibody framework residues affecting the conformation of the hypervariable loops. J. Mol. Biol., 224, 487-499.
33. Banfield, M.J., King, D.J., Mountain, A. and Brady, R.L. (1997) VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs. Proteins, 29, 161-171.
34. Huang, M., Syed, R., Stura, E.A., Stone, M.J., Stefanko, R.S., Ruf, W., Edgington, T.S. and Wilson, I.A. (1998) The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.G9 complex. J. Mol. Biol., 275, 873-894.
35. Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
36. Chailyan, A., Marcatili, P. and Tramontano, A. (2011) The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. FEBS J., 278, 2858-2866.
37. Abhinandan, K.R. and Martin, A.C.R. (2010) Analysis and prediction of VH/VL packing in antibodies. Protein Eng., Des. Sel., 23, 689-697.
38. Stanfield, R., Takimoto-Kamimura, M., Rini, J., Profy, A. and Wilson, I. (1993) Major antigen-induced domain rearrangements in an antibody. Structure, 1, 83-93.