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AbRSA: A robust tool for antibody numbering
dc.contributor.authorLi, Lei
dc.contributor.authorChen, Shuang
dc.contributor.authorMiao, Zhichao
dc.contributor.authorLiu, Yang
dc.contributor.authorLiu, Xu
dc.contributor.authorXiao, Zhi‐xiong
dc.contributor.authorCao, Yang
dc.date.accessioned2019-08-09T17:15:32Z
dc.date.availableWITHHELD_13_MONTHS
dc.date.available2019-08-09T17:15:32Z
dc.date.issued2019-08
dc.identifier.citationLi, Lei; Chen, Shuang; Miao, Zhichao; Liu, Yang; Liu, Xu; Xiao, Zhi‐xiong ; Cao, Yang (2019). "AbRSA: A robust tool for antibody numbering." Protein Science 28(8): 1524-1531.
dc.identifier.issn0961-8368
dc.identifier.issn1469-896X
dc.identifier.urihttps://hdl.handle.net/2027.42/150604
dc.description.abstractThe remarkable progress in cancer immunotherapy in recentâ years has led to the heat of great development for therapeutic antibodies. Antibody numbering, which standardizes a residue index at each position of an antibody variable domain, is an important step in immunoinformatic analysis. It provides an equivalent index for the comparison of sequences or structures, which is particularly valuable for antibody modeling and engineering. However, due to the extremely high diversity of antibody sequences, antibodyâ numbering tools cannot work in all cases. This article introduces a new antibodyâ numbering tool named AbRSA, which integrates heuristic knowledge of regionâ specific features into sequence mapping to enhance the robustness. The benchmarks demonstrate that, AbRSA exhibits robust performance in numbering sequences with diverse lengths and patterns compared with the stateâ ofâ theâ art tools. AbRSA offers a userâ friendly interface for antibody numbering, complementarityâ determining region delimitation, and 3D structure rendering. It is freely available at http://cao.labshare.cn/AbRSA.
dc.publisherJohn Wiley & Sons, Inc.
dc.subject.otherimmunoinformatic
dc.subject.otherantibody
dc.subject.otherantibody numbering
dc.subject.othercomplementarityâ determining region
dc.titleAbRSA: A robust tool for antibody numbering
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/150604/1/pro3633.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/150604/2/pro3633-sup-0001-Suppinfo.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/150604/3/pro3633_am.pdf
dc.identifier.doi10.1002/pro.3633
dc.identifier.sourceProtein Science
dc.identifier.citedreferenceBairoch A, Apweiler R ( 2000 ) The SWISSâ PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28: 45 â 48.
dc.identifier.citedreferenceRoy A, Nair S, Sen N, Soni N, Madhusudhan MS ( 2017 ) In silico methods for design of biological therapeutics. Methods 131: 33 â 65.
dc.identifier.citedreferenceWu TT, Kabat EA ( 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 â 250.
dc.identifier.citedreferenceAlâ Lazikani B, Lesk AM, Chothia C ( 1997 ) Standard conformations for the canonical structures of immunoglobulins. J Mol Biol 273: 927 â 948.
dc.identifier.citedreferenceChothia C, Lesk AM ( 1987 ) Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 196: 901 â 917.
dc.identifier.citedreferenceChothia C, Lesk AM, Tramontano A, Levitt M, Smithâ Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR, Colman PM, Spinelli S, Alzari PM, Poljak RJ ( 1989 ) Conformations of immunoglobulin hypervariable regions. Nature 342: 877 â 883.
dc.identifier.citedreferenceAbhinandan KR, Martin AC ( 2008 ) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol Immunol 45: 3832 â 3839.
dc.identifier.citedreferenceLefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouveninâ Contet V, Lefranc G ( 2003 ) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily Vâ like domains. Dev Comp Immunol 27: 55 â 77.
dc.identifier.citedreferenceHonegger A, Pluckthun A ( 2001 ) Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool. J Mol Biol 309: 657 â 670.
dc.identifier.citedreferenceYe J, Ma N, Madden TL, Ostell JM ( 2013 ) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res 41: W34 â W40.
dc.identifier.citedreferenceZhao S, Lu J ( 2010 ) A germline knowledge based computational approach for determining antibody complementarity determining regions. Mol Immunol 47: 694 â 700.
dc.identifier.citedreferenceNorth B, Lehmann A, Dunbrack RJ ( 2011 ) A new clustering of antibody CDR loop conformations. J Mol Biol 406: 228 â 256.
dc.identifier.citedreferenceOlimpieri PP, Chailyan A, Tramontano A, Marcatili P ( 2013 ) Prediction of siteâ specific interactions in antibodyâ antigen complexes: the proABC method and server. Bioinformatics 29: 2285 â 2291.
dc.identifier.citedreferenceChailyan A, Tramontano A, Marcatili P ( 2012 ) A database of immunoglobulins with integrated tools: DIGIT. Nucleic Acids Res 40: D1230 â D1234.
dc.identifier.citedreferenceSormanni P, Aprile FA, Vendruscolo M ( 2018 ) Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 47: 9137 â 9157.
dc.identifier.citedreferenceMirsky A, Kazandjian L, Anisimova M ( 2015 ) Antibodyâ specific model of amino acid substitution for immunological inferences from alignments of antibody sequences. Mol Biol Evol 32: 806 â 819.
dc.identifier.citedreferenceRego N, Koes D ( 2015 ) 3Dmol.js: molecular visualization with WebGL. Bioinformatics 31: 1322 â 1324.
dc.identifier.citedreferencePundir S, Martin MJ, O’Donovan C ( 2017 ) UniProt protein knowledgebase. Methods Mol Biol 1558: 41 â 55.
dc.identifier.citedreferenceHuang Y, Niu B, Gao Y, Fu L, Li W ( 2010 ) CDâ HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680 â 682.
dc.identifier.citedreferenceBerman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE ( 2000 ) The Protein Data Bank. Nucleic Acids Res 28: 235 â 242.
dc.identifier.citedreferenceZhang Y, Skolnick J ( 2005 ) TMâ align: a protein structure alignment algorithm based on the TMâ score. Nucleic Acids Res 33: 2302 â 2309.
dc.identifier.citedreferenceMarket E, Papavasiliou FN ( 2003 ) V(D)J recombination and the evolution of the adaptive immune system. PLoS Biol 1: e16.
dc.identifier.citedreferenceDiaz M, Casali P ( 2002 ) Somatic immunoglobulin hypermutation. Curr Opin Immunol 14: 235 â 240.
dc.identifier.citedreferenceSwindells MB, Porter CT, Couch M, Hurst J, Abhinandan KR, Nielsen JH, Macindoe G, Hetherington J, Martin AC ( 2017 ) abYsis: integrated antibody sequence and structureâ management, analysis, and prediction. J Mol Biol 429: 356 â 364.
dc.identifier.citedreferenceNeedleman SB, Wunsch CD ( 1970 ) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443 â 453.
dc.identifier.citedreferenceDunbar J, Deane CM ( 2016 ) ANARCI: antigen receptor numbering and receptor classification. Bioinformatics 32: 298 â 300.
dc.identifier.citedreferenceKrawczyk K, Kelm S, Kovaltsuk A, Galson JD, Kelly D, Truck J, Regep C, Leem J, Wong WK, Nowak J, Snowden J, Wright M, Starkie L, Scottâ Tucker A, Shi J, Deane CM ( 2018 ) Structurally mapping antibody repertoires. Front Immunol 9: 1698.
dc.identifier.citedreferenceRiechmann L, Clark M, Waldmann H, Winter G ( 1988 ) Reshaping human antibodies for therapy. Nature 332: 323 â 327.
dc.identifier.citedreferenceVerhoeyen ME, Saunders JA, Broderick EL, Eida SJ, Badley RA ( 1991 ) Reshaping human monoclonal antibodies for imaging and therapy. Dis Markers 9: 197 â 203.
dc.identifier.citedreferenceMarcatili P, Rosi A, Tramontano A ( 2008 ) PIGS: automatic prediction of antibody structures. Bioinformatics 24: 1953 â 1954.
dc.identifier.citedreferenceSircar A, Kim ET, Gray JJ ( 2009 ) RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res 37: W474 â W479.
dc.identifier.citedreferenceKuroda D, Shirai H, Jacobson MP, Nakamura H ( 2012 ) Computerâ aided antibody design. Protein Eng Des Sel 25: 507 â 521.
dc.identifier.citedreferenceShirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K ( 2014 ) Antibody informatics for drug discovery. Biochim Biophys Acta 1844: 2002 â 2015.
dc.identifier.citedreferenceOlimpieri PP, Marcatili P, Tramontano A ( 2015 ) Tabhu: tools for antibody humanization. Bioinformatics 31: 434 â 435.
dc.identifier.citedreferenceJarasch A, Skerra A ( 2017 ) Aligning, analyzing, and visualizing sequences for antibody engineering: automated recognition of immunoglobulin variable region features. Proteins 85: 65 â 71.
dc.identifier.citedreferenceClaveroâ Alvarez A, Di Mambro T, Perezâ Gaviro S, Magnani M, Bruscolini P ( 2018 ) Humanization of antibodies using a statistical inference approach. Sci Rep 8: 14820.
dc.identifier.citedreferenceLeem J, Georges G, Shi J, Deane CM ( 2018 ) Antibody side chain conformations are positionâ dependent. Proteins 86: 383 â 392.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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