1. Shirai, H., Prades, C., Vita, R., Marcatili, P., Popovic, B., Xu, J.,2014. Antibody informatics for drug discovery. Biochimica et Biophysica Acta, 1844: 2002-2015
2. Ranjbar, M.M., ghelianchian, A., nazoktabar, A., ahmadi, N., khoshnevisan, R.,2013. Immunoinformatics and epitope prediction methods dynamic science with promising achievements. J of Ilam University of med Sc, 21 ,6:300-309.
3. Ranjbar, M.M., Ahmadi, N.A., Ghorban, K.h., Ghalyanchi Langeroudi. A., Dadmanesh, M., Amini, H.R., Sedighi Moghaddam, B.,2014. Immnoinformatics: novel view in understanding of immune system function, databases and prediction of immunogenic epitopes. 17: 1.
4. Motamed, N.,2013. Experimental infection with avian influenza virus subtype H9N2 in broiler chicks infected with infectious bursal disease virus. Shahid Chamran University. Ahvaz, Iran.
5. Abbas, A.K., Lichtman, A.H., and Pillai, S.,2015. Cellular and molecular immunology. 8th edition. Chapter 5:Antibody and Antigens. Publisher Elsevier,87-106.
6. Ranjbar, M.M., Malekan, M., Mirabad, M.M.,2012. Nanobodies: Evalution structure, benefits and applications. 1: 21-26.
7. Teng, G., Papavasiliou, F.N.,2007. Immunoglobulin somatic hypermutation. Annu Rev Genet ,41:107–120.
8. Kuroda, D., Shirai, H., Kobori, M., Nakamura, H.,2008. Structural classification of CDR-H3 revisited: a lesson in antibody modeling, 73: 608–620.
9. Jawa, V., Cousens, L.P., Awwad, M., Wakshull, E., Kropshofer, H., De Groot, A.S.,2013. T-cell dependent immunogenicity of protein therapeutics: preclinical assessment and mitigation. Clin Immunol,149: 534–555.
10. Reddy, S.T., Ge, X., Miklos, A.E., Hughes, R.A., Kang, S.H., Hoi, K.H., 2010. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat Biotechnol , 28: 965–969.
11. Esmaielbeiki, R., Krawczyk, K., Knapp, B., Nebel, J.C., and Deane, C.M.,2015. Progress and challenges in predicting protein interfaces. Brief in Bioinfo : 1–15.
12. Kringelum, J.V., Lundegaard, C., Lund, O., Nielsen, M.,2012. Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol, 8: e1002829.
13. Ramaraj, T., Angel, T., Dratz, E.A., Jesaitis, A.J., Mumey, B.,2012. Antigen-antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures. Biochim Biophys Acta, 1824(3): 520–532.
14. Al-Lazikani, B., Lesk, A.M., Chothia, C.,1997. Standard conformations for the canonical structures of immunoglobulins. J Mol Biol, 273:927–948.
15. Zemlin, M., Klinger, M., Link, J., Zemlin, C., Bauer, K., Engler, J.A., Schroeder, H.W., Kirkham, P.M.,2003. Expressed murine and human cdr-h3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures. J Mol Biol, 334(4): 733-749.
16. Miklos, E., Kluwe, C., Der, S., Pai, S., Sircar, A., Hughes, A., 2012. Structure-based design of supercharged, highly thermoresistant antibodies. Chem Biol, 19: 449–455.
17. Xu, J., Tack, D., Hughes, A., Ellington, D., Gray, J.,2014. Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex. J Struct Biol, 185: 215–222.
18. Kiyoshi, M., Caaveiro, M., Miura, E., Nagatoishi, S., Nakakido, M., Soga, S,.2014. Affinity improvement of a therapeutic antibody by structurebased computational design: generation of electrostatic interactions in the transition state stabilizes the antibody–antigen complex. PLoS One, 9e87099.
19. Tharakaraman, K., Robinson, N., Hatas, A., Chen, L., Siyue, L., Raguram, S., 2013. Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency. Proc Natl Acad Sci, 110: 1555–64.
20. Chothia, C., Lesk, M., Tramontano, A., Levitt, M., Smith-Gill, J., Air, G.,1989. Conformations of immunoglobulin hypervariable regions. Nature, 342: 877–883.
21. North, B., Lehmann, A., Dunbrack, R.L,2011. A new clustering of antibody CDR loop conformation. J Mol Biol, 406: 228–256.
22. Chailyan, A., Marcatili, P., Cirillo, D., Tramontano, A.,2011. Structural repertoire of immunoglobulin lambda light chains. Proteins, 79: 1513–1524.
23. Verdino, P., Witherden, D.A., Podshivalova, K., Rieder, S.E., Havran, W.L., Wilson, I.A.,2011. cDNA sequence and Fab crystal structure of HL4E10, a hamster IgG lambda light chain antibody stimulatory for gammadelta T cells. PLoS One, 6e19828.
24. Sircar, A., Sanni, K.A., Shi, J., Gray, J.J., 2011. Analysis and modeling of the variable region of camelid single-domain antibodies. J Immunol, 186: 6357–67.
25. Whitelegg, NR., Rees, A.R.,2000. WAM: an improved algorithm for modelling antibodies on the WEB. Protein Eng, 13: 819–824.
26. Zhao, Z., Worthylake, D., LeCour, J., Maresh, G.A., Pincus, S.H., 2012. Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody. PLoS One,7,12:e52613.
27. Holm, L., Laaksonen, L., Kaartinen, M., Teeri, T., Knowles, J.K.,1990. Molecular modeling study of antigen binding to oxazolone-specific antibodies: the Ox1 idiotypic IgG and its mature variant with increased affinity to 2-phenyloxazolone. Protein Eng, 3: 403–409.
28. Martin, A.C., Cheetham, J.C., Rees, A.R.,1989. Modeling antibody hypervariable loops: a combined algorithm. Proc Natl Acad Sci, 86: 9268–72.
29. Kunik, V., Peters, B., Ofran, Y.,2012. Structural consensus among antibodies defines the antigen binding site. PLoS Comput Biol,8:e1002388.
30. Morea, V., Tramontano, A., Rustici, M., Chothia, C., Lesk, A.M.,1998. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol, 275:269–294.
31. Choi, Y., Deane, C.M.,2011. Predicting antibody complementarity determining region structures without classification. Mol Biosyst, 7: 3327–34.
32. Sela-Culang, I., Alon, S., Ofran, Y.,2012. A systematic comparisonof free andboundantibodies reveals binding-related conformational changes. J Immunol, 189: 4890–99.
33. Zhu, K., Pincus, D.L., Zhao, S., Friesner, R.A.,2006. Long loop prediction using the protein local optimization program. Proteins, 65: 438–452.
34. Dunbar, J., Fuchs, A., Shi, J., Deane, C.M.,2013. ABangle: characterising the VH–VL orientation in antibodies. Protein Eng Des Sel, 26: 611–620.
35. Waldmann, H., and Hale, G.,2005. CAMPATH: from concept to clinic. Philos Trans R Soc Lond B Biol Sci, 29: 1707-11.
36. Novotný, J., Handschumacher, M., Haber, E., Bruccoleri, R.E., Carlson, B., Fanning, W., 1986. Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains). Proc Natl Acad Sci, 83(2):226-30.
37. Hu, W.G., Yin, J., Chau, D., Negrych, L.M., Cherwonogrodzky, J.W., 2012.Humanization and characterization of an anti-ricin neutralization monoclonal antibody. PLoS One. 7,9:e45595.
38. Sundberg, E.J., Urrutia, M., Braden, B.C., Isern, J., Tsuchiya, D., Fields, B.A., 2000. Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. Biochemistry, 39:15375–87.
39. Moreira, I.S., Fernandes, P.A., Ramos, M.J.,2007. Hot spot computational identification: application to the complex formed between the hen eggwhite lysozyme (HEL) and the antibody HyHEL-10. Int J Quantum Chem, 107:299–310.
40. Wang. X., Das. T.K., Singh. S.K., Kumar, S.,2009. Potential aggregation prone regions in biotherapeutics: a survey of commercial monoclonal antibodies. MAbs, 1: 254–267.
41. Brenke, R., Hall, D.R., Chuang, G.Y., Comeau, S.R., Bohnuud, T., Beglov, D., 2012. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics, 28:2608–14.
42. Beck, A., Wagner-Rousset, E., Ayoub, D., Van, D.A., Sanglier-Cianferani, S.,2013. Characterization of therapeutic antibodies and related products. Anal Chem, 85: 715–36.
43. Simpson, R.J.,2010. Stabilization of proteins for storage. Cold Spring Harb Protoc 2010; 5 doi:10.1101/pdb.top79.
44. Wakankar, A.A., Liu, J., Vandervelde, D., Wang, Y.J., Shire, S.J., Borchardt, R.T., 2007. The effect of cosolutes on the isomerization of aspartic acid residues and conformational stability in a monoclonal antibody. J Pharm Sci, 96: 1708–18.
45. Huang, L., Lu, J., Wroblewski, V.J., Beals, J.M., Riggin, R.M.,2005. In vivo deamidation characterization of monoclonal antibody by LC/MS/MS. Anal Chem 2005; 77: 1432–39.
46. Yan, B., Steen, S., Hambly, D., Valliere-Douglass, J., Vanden, B.T., Smallwood, S., 2009. Succinimide formation at Asn 55 in the complementarity determining region of a recombinant monoclonal antibody IgG1 heavy chain. J Pharm Sci, 98: 3509– 3521.
47. Kosky, A.A., Dharmavaram, V., Ratnaswamy, G., Manning, M.C., 2009. Multivariate analysis of the sequence dependence of asparagine deamidation rates in peptides. Pharm Res, 26: 2417–2428.
48. Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D.,2009. Outcome of a workshop on applications of protein models in biomedical research. Structure ,17: 151–159.
49. Motedayen, M., Nikbakht, G., Rasaee, M., Zare Mirakabadi, A.,2015. Construction of a human recombinant polyclonal Fab fragment antibody library using peripheral blood lymphocytes of snake bitten victims. Archives of Razi institute, 70,4 : 255-261.
)
