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Volumn 82, Issue 8, 2014, Pages 1563-1582

Antibody modeling assessment II. Structures and models

Author keywords

Canonical structure; CDR; Crystal structure; Structure prediction; VL VH packing

Indexed keywords

AMINO ACID SEQUENCE; ANTIBODY STRUCTURE; ARTICLE; CRYSTAL STRUCTURE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN DATABASE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; COMPLEMENTARITY DETERMINING REGION; HUMAN; IMMUNOGLOBULIN VARIABLE REGION; ISOMERISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

EID: 84904515208     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24554     Document Type: Article
Times cited : (64)

References (50)
  • 1
    • 84858144476 scopus 로고    scopus 로고
    • Methods for the homology modeling of antibody variable regions
    • Sircar A. Methods for the homology modeling of antibody variable regions. Methods Mol Biol 2012;857:301-311.
    • (2012) Methods Mol Biol , vol.857 , pp. 301-311
    • Sircar, A.1
  • 2
    • 84867833519 scopus 로고    scopus 로고
    • Computer-assisted modeling of antibody variable domains
    • Ramos OH. Computer-assisted modeling of antibody variable domains. Methods Mol Biol 2012;907:39-55.
    • (2012) Methods Mol Biol , vol.907 , pp. 39-55
    • Ramos, O.H.1
  • 6
    • 0023278330 scopus 로고
    • Canonical structures for the hypervariable regions of immunoglobulins
    • Chothia C, Lesk A. Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 1987;196:901-917.
    • (1987) J Mol Biol , vol.196 , pp. 901-917
    • Chothia, C.1    Lesk, A.2
  • 8
    • 77956016509 scopus 로고    scopus 로고
    • Analysis and prediction of VH/VL packing in antibodies
    • Abhinandan KR, Martin AC. Analysis and prediction of VH/VL packing in antibodies. Protein Eng Des Sel 2010;23:689-697.
    • (2010) Protein Eng Des Sel , vol.23 , pp. 689-697
    • Abhinandan, K.R.1    Martin, A.C.2
  • 9
    • 0020977127 scopus 로고
    • Structural basis of antibody function
    • Davies DR, Metzger H. Structural basis of antibody function. Annu Rev Immunol 1983;1:87-117.
    • (1983) Annu Rev Immunol , vol.1 , pp. 87-117
    • Davies, D.R.1    Metzger, H.2
  • 10
    • 0018064944 scopus 로고
    • The structural basis of antibody complementarity
    • Kabat EA. The structural basis of antibody complementarity. Adv Protein Chem 1978;32:1-75.
    • (1978) Adv Protein Chem , vol.32 , pp. 1-75
    • Kabat, E.A.1
  • 11
    • 0034426867 scopus 로고    scopus 로고
    • Antibody modeling: implications for engineering and design
    • Morea V, Lesk AM, Tramontano A. Antibody modeling: implications for engineering and design. Methods 2000;20:267-279.
    • (2000) Methods , vol.20 , pp. 267-279
    • Morea, V.1    Lesk, A.M.2    Tramontano, A.3
  • 12
    • 0028984808 scopus 로고
    • Prediction of hypervariable CDR-H3 loop structures in antibodies
    • Reczko M, Martin AC, Bohr H, Suhai S. Prediction of hypervariable CDR-H3 loop structures in antibodies. Protein Eng 1995;8:389-395.
    • (1995) Protein Eng , vol.8 , pp. 389-395
    • Reczko, M.1    Martin, A.C.2    Bohr, H.3    Suhai, S.4
  • 13
    • 0032536197 scopus 로고    scopus 로고
    • Conformations of the third hypervariable region in the VH domain of immunoglobulins
    • Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol 1998;275:269-294.
    • (1998) J Mol Biol , vol.275 , pp. 269-294
    • Morea, V.1    Tramontano, A.2    Rustici, M.3    Chothia, C.4    Lesk, A.M.5
  • 14
    • 0030577371 scopus 로고    scopus 로고
    • Structural classification of CDR-H3 in antibodies
    • Shirai H, Kidera A, Nakamura H. Structural classification of CDR-H3 in antibodies. FEBS Lett 1996;399:1-8.
    • (1996) FEBS Lett , vol.399 , pp. 1-8
    • Shirai, H.1    Kidera, A.2    Nakamura, H.3
  • 15
    • 0032568959 scopus 로고    scopus 로고
    • Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction
    • Oliva B, Bates PA, Querol E, Avilés FX, Sternberg MJ. Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J Mol Biol 1998;279:1193-1210.
    • (1998) J Mol Biol , vol.279 , pp. 1193-1210
    • Oliva, B.1    Bates, P.A.2    Querol, E.3    Avilés, F.X.4    Sternberg, M.J.5
  • 16
    • 57349097173 scopus 로고    scopus 로고
    • Structural classification of CDR-H3 revisited: a lesson in antibody modeling
    • Kuroda D, Shirai H, Kobori M, Nakamura H. Structural classification of CDR-H3 revisited: a lesson in antibody modeling. Proteins 2008;73:608-620.
    • (2008) Proteins , vol.73 , pp. 608-620
    • Kuroda, D.1    Shirai, H.2    Kobori, M.3    Nakamura, H.4
  • 17
    • 67849111558 scopus 로고    scopus 로고
    • RosettaAntibody: antibody variable region homology modeling server
    • Sircar A, Kim ET, Gray JJ. RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res 2009;37:W474-W479.
    • (2009) Nucleic Acids Res , vol.37
    • Sircar, A.1    Kim, E.T.2    Gray, J.J.3
  • 18
    • 80755125384 scopus 로고    scopus 로고
    • Predicting antibody complementarity determining region structures without classification
    • Choi Y, Deane CM. Predicting antibody complementarity determining region structures without classification. Mol Biosyst 2011;7:3327-3334.
    • (2011) Mol Biosyst , vol.7 , pp. 3327-3334
    • Choi, Y.1    Deane, C.M.2
  • 19
    • 84878147881 scopus 로고    scopus 로고
    • Ab initio structure prediction of the antibody hypervariable H3 loop
    • Zhu K, Day T. Ab initio structure prediction of the antibody hypervariable H3 loop. Proteins 2013;81:1081-1089.
    • (2013) Proteins , vol.81 , pp. 1081-1089
    • Zhu, K.1    Day, T.2
  • 20
    • 50549090182 scopus 로고    scopus 로고
    • PIGS: automatic prediction of antibody structures
    • Marcatili P, Rosi A, Tramontano A. PIGS: automatic prediction of antibody structures. Bioinformatics 2008;24:1953-1954.
    • (2008) Bioinformatics , vol.24 , pp. 1953-1954
    • Marcatili, P.1    Rosi, A.2    Tramontano, A.3
  • 21
    • 79251598995 scopus 로고    scopus 로고
    • A new clustering of antibody CDR loop conformations
    • North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011;406:228-256.
    • (2011) J Mol Biol , vol.406 , pp. 228-256
    • North, B.1    Lehmann, A.2    Dunbrack, R.L.3
  • 22
    • 48049124972 scopus 로고    scopus 로고
    • Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains
    • 2008
    • Abhinandan KR, Martin AC. 2008. Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol Immunol 2008;45:3832-3839.
    • (2008) Mol Immunol , vol.45 , pp. 3832-3839
    • Abhinandan, K.R.1    Martin, A.C.2
  • 26
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • A
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr 1976;A32:922-923.
    • (1976) Acta Crystallogr , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 27
    • 0033593356 scopus 로고    scopus 로고
    • Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire
    • de Wildt RM, Hoet RM, van Venrooij WJ, Tomlinson IM, Winter G. Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire. J Mol Biol 1999;285:895-901.
    • (1999) J Mol Biol , vol.285 , pp. 895-901
    • de Wildt, R.M.1    Hoet, R.M.2    van Venrooij, W.J.3    Tomlinson, I.M.4    Winter, G.5
  • 29
    • 84885010253 scopus 로고    scopus 로고
    • ABangle: characterising the VH-VL orientation in antibodies
    • Dunbar J, Fuchs A, Shi J, Deane CM. ABangle: characterising the VH-VL orientation in antibodies. Protein Eng Des Sel 2013;26:611-620.
    • (2013) Protein Eng Des Sel , vol.26 , pp. 611-620
    • Dunbar, J.1    Fuchs, A.2    Shi, J.3    Deane, C.M.4
  • 33
    • 84871310960 scopus 로고    scopus 로고
    • Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody
    • Zhao Z, Worthylake D, LeCour L Jr, Maresh GA, Pincus SH. Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody. PLoS One 2012;7:e52613.
    • (2012) PLoS One , vol.7
    • Zhao, Z.1    Worthylake, D.2    LeCour Jr., L.3    Maresh, G.A.4    Pincus, S.H.5
  • 36
    • 67349207370 scopus 로고    scopus 로고
    • Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains
    • Narayanan A, Sellers BD, Jacobson MP. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. J Mol Biol 2009;388:941-953.
    • (2009) J Mol Biol , vol.388 , pp. 941-953
    • Narayanan, A.1    Sellers, B.D.2    Jacobson, M.P.3
  • 37
    • 78649795438 scopus 로고    scopus 로고
    • Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody
    • Freeman MM, Seaman MS, Rits-Volloch S, Hong X, Kao CY, Ho DD, Chen B. Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody. Structure 2010;18:1632-1641.
    • (2010) Structure , vol.18 , pp. 1632-1641
    • Freeman, M.M.1    Seaman, M.S.2    Rits-Volloch, S.3    Hong, X.4    Kao, C.Y.5    Ho, D.D.6    Chen, B.7
  • 38
    • 83755195810 scopus 로고    scopus 로고
    • Stable coordination of the inhibitory Ca2+ ion at the metal ion-dependent adhesion site in integrin CD11b/CD18 by an antibody-derived ligand aspartate: implications for integrin regulation and structure-based drug design
    • Mahalingam B, Ajroud K, Alonso JL, Anand S, Adair BD, Horenstein AL, Malavasi F, Xiong JP, Arnaout MA. Stable coordination of the inhibitory Ca2+ ion at the metal ion-dependent adhesion site in integrin CD11b/CD18 by an antibody-derived ligand aspartate: implications for integrin regulation and structure-based drug design. J Immunol 2011;187:6393-6401.
    • (2011) J Immunol , vol.187 , pp. 6393-6401
    • Mahalingam, B.1    Ajroud, K.2    Alonso, J.L.3    Anand, S.4    Adair, B.D.5    Horenstein, A.L.6    Malavasi, F.7    Xiong, J.P.8    Arnaout, M.A.9
  • 39
    • 0033080945 scopus 로고    scopus 로고
    • Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs
    • Stanfield R, Cabezas E, Satterthwait A, Stura E, Profy A, Wilson I. Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Structure 1999;7:131-142.
    • (1999) Structure , vol.7 , pp. 131-142
    • Stanfield, R.1    Cabezas, E.2    Satterthwait, A.3    Stura, E.4    Profy, A.5    Wilson, I.6
  • 41
    • 0032769692 scopus 로고    scopus 로고
    • Structure of an activity suppressing Fab fragment to cytochrome P450 aromatase: insights into the antibody-antigen interactions
    • Sawicki MW, Ng PC, Burkhart BM, Pletnev VZ, Higashiyama T, Osawa Y, Ghosh D. Structure of an activity suppressing Fab fragment to cytochrome P450 aromatase: insights into the antibody-antigen interactions. Mol Immunol 1999;36:423-432.
    • (1999) Mol Immunol , vol.36 , pp. 423-432
    • Sawicki, M.W.1    Ng, P.C.2    Burkhart, B.M.3    Pletnev, V.Z.4    Higashiyama, T.5    Osawa, Y.6    Ghosh, D.7
  • 42
    • 0025063143 scopus 로고
    • Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins
    • Tramontano A, Chothia C, Lesk AM. 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 1990;215:175-182.
    • (1990) J Mol Biol , vol.215 , pp. 175-182
    • Tramontano, A.1    Chothia, C.2    Lesk, A.M.3
  • 44
    • 34848850459 scopus 로고    scopus 로고
    • Structural plasticity in Ig superfamily domain 4 of ICAM-1 mediates cell surface dimerization
    • Chen X, Kim TD, Carman CV, Mi LZ, Song G, Springer TA. Structural plasticity in Ig superfamily domain 4 of ICAM-1 mediates cell surface dimerization. Proc Natl Acad Sci USA 2007;104:15358-15363.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 15358-15363
    • Chen, X.1    Kim, T.D.2    Carman, C.V.3    Mi, L.Z.4    Song, G.5    Springer, T.A.6
  • 45
    • 0028304866 scopus 로고
    • Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2
    • Tormo J, Blaas D, Parry NR, Rowlands D, Stuart D, Fita I. Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. EMBO J 1994;13:2247-2256.
    • (1994) EMBO J , vol.13 , pp. 2247-2256
    • Tormo, J.1    Blaas, D.2    Parry, N.R.3    Rowlands, D.4    Stuart, D.5    Fita, I.6
  • 48
    • 59449096415 scopus 로고    scopus 로고
    • Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking
    • Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ. Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins 2009;74:497-514.
    • (2009) Proteins , vol.74 , pp. 497-514
    • Sivasubramanian, A.1    Sircar, A.2    Chaudhury, S.3    Gray, J.J.4
  • 49
    • 33645049294 scopus 로고    scopus 로고
    • Antibody elbow angles are influenced by their light chain class
    • Stanfield RL, Zemla A, Wilson IA, Rupp B. Antibody elbow angles are influenced by their light chain class. J Mol Biol 2006;357:1566-1574.
    • (2006) J Mol Biol , vol.357 , pp. 1566-1574
    • Stanfield, R.L.1    Zemla, A.2    Wilson, I.A.3    Rupp, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.