Computer-assisted modeling of antibody variable domains

Methods in Molecular Biology

Volumn 907, Issue , 2012, Pages 39-55

  Ramos, Oscar H P ^a  

^a SERVICE DE CHIMIE BIOORGANIQUE ET DE MARQUAGE   (France)

Author keywords

Antibody; Antigen combining site; Modeling; Structure prediction; Variable domains

Indexed keywords

EID: 84867833519     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-974-7_2     Document Type: Article

References (33)

1. Whitelegg NR, Rees AR (2000) Wam: an improved algorithm for modelling antibodies on the web. Protein Eng 13:819-824
2. Sircar A, Kim ET, Gray JJ (2009) Rosettaantibody: antibody variable region homology modeling server. Nucleic Acids Res 37:W474-W479
3. Marcatili P, Rosi A, Tramontano A (2008) Pigs: automatic prediction of antibody structures. Bioinformatics 24:1953-1954
4. Kabat EA, Wu TT (1991) Identical v region amino acid sequences and segments of sequences in antibodies of different speci fi cities. relative contributions of vh and vl genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites. J Immunol 147:1709-1719
5. Chothia C, Lesk AM (1987) Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 196:901-917
6. Al-Lazikani B, Lesk AM, Chothia C (1997) Standard conformations for the canonical structures of immunoglobulins. J Mol Biol 273:927-948
7. Abhinandan KR, Martin ACR (2008) Analysis and improvements to kabat and structurally correct numbering of antibody variable domains. Mol Immunol 45:3832-3839
8. Honegger A, Plückthun A (2001) Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool. J Mol Biol 309:657-670
9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
10. Guex N, Peitsch MC (1997) Swiss-model and the swiss-pdbviewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723
11. Abhinandan KR, Martin ACR (2010) Analysis and prediction of vh/vl packing in antibodies. Protein Eng Des Sel 23:689-697
12. Canutescu AA, Dunbrack RLJ (2003) Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 12: 963-972
13. Mandell DJ, Coutsias EA, Kortemme T (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6:551-552
14. Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J (2010) Practically useful: what the rosetta protein modeling suite can do for you. Biochemistry 49:2987-2998
15. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) Gromacs: fast, fl exible, and free. J Comput Chem 26:1701-1718
16. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K (2005) Scalable molecular dynamics with namd. J Comput Chem 26:1781-1802
17. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Ca fl isch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) Charmm: the biomolecular simulation program. J Comput Chem 30:1545-1614
18. Martin AC, Cheetham JC, Rees AR (1989) Modeling antibody hypervariable loops: a combined algorithm. Proc Natl Acad Sci U S A 86:9268-9272
19. Bruccoleri RE, Karplus M (1987) Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26:137-168
20. Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773
21. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) Procheck: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283-291
22. Vriend G (1990) What if: a molecular modeling and drug design program. J Mol Graph 8(52-6):29
23. Schrödinger L The pymol molecular graphics system
24. Humphrey W, Dalke A, Schulten K (1996) Vmd: visual molecular dynamics. J Mol Graph 14(33-8):27-28
25. Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM (1998) Conformations of the third hypervariable region in the vh domain of immunoglobulins. J Mol Biol 275: 269-294
26. Shirai H, Kidera A, Nakamura H (1996) Structural classi fi cation of cdr-h3 in antibodies. FEBS Lett 399:1-8
27. Kuroda D, Shirai H, Kobori M, Nakamura H (2008) Structural classi fi cation of cdr-h3 revisited: a lesson in antibody modeling. Proteins 73:608-620
28. Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ (2009) Toward high-resolution homology modeling of antibody fv regions and application to antibody-antigen docking. Proteins 74:497-514
29. Martin AC, Thornton JM (1996) Structural families in loops of homologous proteins: automatic classi fi cation, modelling and application to antibodies. J Mol Biol 263:800-815
30. Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR et al (1989) Conformations of immunoglobulin hypervariable regions. Nature 342:877-883
31. Barré S, Greenberg AS, Flajnik MF, Chothia C (1994) Structural conservation of hypervariable regions in immunoglobulins evolution. Nat Struct Biol 1:915-920
32. Tomlinson IM, Cox JP, Gherardi E, Lesk AM, Chothia C (1995) The structural repertoire of the human v kappa domain. EMBO J 14:4628-4638
33. Chothia C, Lesk AM, Gherardi E, Tomlinson IM, Walter G, Marks JD, Llewelyn MB, Winter G (1992) Structural repertoire of the human vh segments. J Mol Biol 227:799-817