**Author details**

Tania M. Manieri1 \*, Carolina G. Magalhaes1 , Daniela Y. Takata1 , João V. Batalha-Carvalho1 and Ana M. Moro1,2

1 Biopharmaceuticals Lab, Butantan Institute, Sao Paulo, Brazil

2 iii/INCT, São Paulo, Brazil

\*Address all correspondence to: tania.manieri@butantan.gov.br

© 2020 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**119**

In silico *Techniques for Prospecting and Characterizing Monoclonal Antibodies*

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics.

[10] Leem J, Dunbar J, Georges G, Shi J, Deane CM. ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation. mAbs.

[11] Klausen MS, Anderson MV, Jespersen MC, Nielsen M, Marcatili *P. LYRA*, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Res. 2015;43(W1):W349-55.

[12] Schritt D, Li SL, Rozewicki J, Katoh K, Yamashita K, Volkmuth W, et al. Repertoire Builder: high-throughput

structural modeling of B and T cell receptors. Mol Syst Des Eng.

[13] Lyskov S, Chou FC, Conchuir SO, Der BS, Drew K, Kuroda D, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS

[14] Leem J, Georges G, Shi J, Deane CM. Antibody side chain conformations are position-dependent. Proteins.

[16] Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS. BetaSCPWeb: sidechain prediction for protein structures using Voronoi diagrams and geometry prioritization. Nucleic Acids Research.

[15] Krivov GG, Shapovalov MV, Dunbrack RL, Jr. Improved prediction of protein side-chain conformations

with SCWRL4. Proteins. 2009;77(4):778-95.

2016;44(W1):W416-W23.

[17] Choi Y, Deane CM. FREAD revisited: Accurate loop structure

2017;33(9):1346-53.

2016;8:1259-68.

2019;4(4):761-8.

One. 2013;8(5):e63906.

2018;86(4):383-92.

*DOI: http://dx.doi.org/10.5772/intechopen.94366*

[2] Boyd SD, Joshi SA. High-Throughput DNA Sequencing Analysis of Antibody

[1] Rees AR. Understanding the human antibody repertoire. MAbs.

Repertoires. Microbiol Spectr.

[3] Schroeder HW, Jr. Similarity and divergence in the development and expression of the mouse and human antibody repertoires. Dev Comp Immunol. 2006;30(1-2):119-35.

[4] Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The Protein Data Bank. Nucleic Acids

[5] Lefranc MP, Pommie C, Kaas Q, Duprat E, Bosc N, Guiraudou D, et al. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Developmental and comparative immunology.

[6] Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic

[7] Brochet X, Lefranc MP, Giudicelli V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 2008;36(Web Server issue):W503-8.

Bonvin A, Colwell LJ, Kelm S, Kumar S, et al. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief

[9] Marks C, Nowak J, Klostermann S, Georges G, Dunbar J, Shi J, et al.

Acids Res. 2013;41(Web Server

[8] Norman RA, Ambrosetti F,

Res. 2000;28(1):235-42.

2005;29(3):185-203.

issue):W34-40.

Bioinform. 2019.

2020;12(1):1729683.

**References**

2014;2(5).

In silico *Techniques for Prospecting and Characterizing Monoclonal Antibodies DOI: http://dx.doi.org/10.5772/intechopen.94366*
