Towards the chemometric dissection of peptide - HLA-A*0201 binding affinity: Comparison of local and global QSAR models

Journal of Computer-Aided Molecular Design

Volumn 19, Issue 3, 2005, Pages 203-212

  Doytchinova, Irini A ^a   Walshe, Valerie ^a   Borrow, Persephone ^a   Flower, Darren R ^a  

^a EDWARD JENNER INST FOR VACC RES   (United Kingdom)

Author keywords

GA; Peptides; PLS; Stepwise regression; z scales

Indexed keywords

AMINO ACIDS; BINDING ENERGY; COMPUTATIONAL CHEMISTRY; GENETIC ALGORITHMS; MOLECULAR GRAPHICS; MOLECULES;

AMINO-ACIDS; CHEMOMETRICES; GA; GLOBAL DESCRIPTORS; HLA-A*0201; LOCAL DESCRIPTORS; PLS; QSAR MODEL; STEPWISE REGRESSION; Z-SCALE;

PEPTIDES;

AMINO ACID; HLA A ANTIGEN;

ANALYSIS OF VARIANCE; ARTICLE; BINDING AFFINITY; CHEMOMETRIC ANALYSIS; FLUORESCENCE ACTIVATED CELL SORTING; GENETIC ALGORITHM; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR WEIGHT; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; VALIDATION PROCESS;

EID: 22144474037     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-005-3993-x     Document Type: Article

References (30)

1. A. Sette A. Vitiello B. Reherman P. Fowler R. Nayersina W.M. Kast C.J. Melief C. Oseroff L. Yuan J. Ruppert J. Sidney M.F. Delguercio S. Southwood R.T. Kubo R.W. Chestnut H.M. Grey and F.V. Chisari 1994 J. Immunol. 153 55861:CAS:528:DyaK2MXis12ksbs%3D 7527444
2. S. Krebs and D. Rognan 1998 Pharm. Acta Helv. 73 17310.1016/ S0031-6865(98)00021-1 1:CAS:528:DyaK1cXntlyqsrY%3D 9861866
3. W.J. Pichler 2002 Toxicology 181-182 4910.1016/S0300-483X(02)00254-8 12505284
4. J.P. Griffith J.L. Kim E.E. Kim M.D. Sintchak J.A. Thomson M.J. Fitzgibbon M.A. Fleming P.R. Caron K. Hsiao and M.A. Navia 1995 Cell 82 50710.1016/0092-8674(95)90439-5 1:CAS:528:DyaK2MXnsFSgtrY%3D 7543369
5. S.G.E. Marsh J.G. Bodmer E.D. Albert W.F. Bodmer R.E. Bontrop S. Dupont H.A. Erlich J.A. Hansen B. Mach W.R. Mayr P. Parham E.W. Petersdorf T. Sasazuki G.M.T. Schreuder J.L. Strominger A. Svejgaard and P.I. Terasaki 2001 Eur. J. Immunogen. 28 37710.1046/j.1365-2370.2001.00268.x 1:CAS:528:DC%2BD3MXls1Wqu7w%3D 11422419
6. J. Bodmer 1996 Ciba Found. Symp. 197 2331:STN:280:BymH38vpt1I%3D 8827377
7. G.E. Peoples P.S. Goedegebuure R. Smith D.C. Linehan I. Yoshino and T.Y. Eberlein 1995 Proc. Natl. Acad. Sci. USA 92 4321:CAS:528:DyaK2MXjt12qsbo%3D 7831305
8. A.J. McMichael P. Parham F.M. Brodsky and J.R. Pilch 1980 J. Exp. Med. 152 Suppl. 2 195
9. Y. Rongcun F. Salazar-Onfray J. Charo K.-J. Malmberg K. Evrin H. Maes C. Hising M. Petersson O. Larsson L. Lan E. Appella A. Sette E. Celis and R. Kiessling 1999 J. Immunol. 163 10371:CAS:528:DyaK1MXksVens7g%3D 10395702
10. L. Rivoltini Y. Kawakami K. Sakaguchi S. Southwood A. Sette P.F. Robbins F.M. Marincola M.L. Salgaller J.R. Yannelli E. Appella and S.A. Rosenberg 1995 J. Immunol. 154 22571:CAS:528:DyaK2MXjsl2qur4%3D 7868898
11. M.A. Saper P.J. Bjorkman and D.D. Wiley 1991 J. Mol. Biol. 219 27710.1016/0022-2836(91)90567-P 1:CAS:528:DyaK3MXkvFSgtbw%3D 2038058
12. D.R. Madden D.N. Garboczi and D.C. Wiley 1993 Cell 75 69310.1016/ 0092-8674(93)90490-H 1:CAS:528:DyaK2cXivV2hsQ%3D%3D 7694806
13. J. Ruppert J. Sidney E. Celis R.T. Kubo H.M. Grey and A. Sette 1993 Cell 74 92910.1016/0092-8674(93)90472-3 1:CAS:528:DyaK3sXms1yns7k%3D 8104103
14. D.R. Madden 1995 Annu. Rev. Immunol. 13 5871:CAS:528:DyaK2MXltFamurY%3D 7612235
15. I.A. Doytchinova M.J. Blythe and D.R.J. Flower 2002 Proteome Res. 1 26310.1021/pr015513z 1:CAS:528:DC%2BD38Xislags7o%3D
16. I.A. Doytchinova V.A. Walshe N.A. Jones S.E. Gloster P. Borrow and D.R. Flower 2004 J. Immunol. 172 74951:CAS:528:DC%2BD2cXks1ahu78%3D 15187128
17. M. Sandberg L. Eriksson J. Jonsson M. Sjöström and S. Wold 1998 J. Med. Chem. 41 248110.1021/jm9700575 1:CAS:528:DyaK1cXktlShuro%3D 9651153
18. SYBYL 6.9. Tripos Inc., 1699 Hanley Road, St. Louis, MO 63144
19. MDL QSAR 2.2. 14600 Catalina St. San Leandro CA 94577
20. G. Stuber S. Modrow P. Hoglund L. Franksson J. Elvin H. Wolf K. Karre and G. Klein 1992 Eur. J. Immunol. 22 26971:CAS:528:DyaK3sXlsFSj 1327802
21. A.R. Lopes A. Jaye L. Dorrell S. Sabally A. Alabi N.A. Jones D.R. Flower A. Groot De P. Newton R.M. Lascar I. Williams H. Whittle A. Bertoletti P. Borrow and M.K. Maini 2003 J. Immunol. 171 3071:CAS:528:DC%2BD3sXks12jtLg%3D 12817012
22. Y. Chen J. Sidney S. Southwood A.L. Cox K. Sakaguchi R.A. Henderson E. Appella D.F. Hunt A. Sette and V.H. Engelhard 1994 J. Immunol. 152 28741:CAS:528:DyaK2cXis1OltL0%3D 8144888
23. Daylight. Theory Manual at http://www.daylight.com/release/f_manuals.html
24. Hall, L.H. and Kier, L.B., In Devillers, J. (Ed.), Methods for QSAR Modeling, Gordon and Breach, London, 1999, pp
25. Hall, L.H. and Kier, L.B., In Devillers, J. (Ed.), Topological Indices and Related Descriptors in QSAR and QSPR, Gordon and Breach, London, 1999, pp
26. S. Hellberg M. Sjöström and S. Wold 1986 Acta Chem. Scand. B40 1351:CAS:528:DyaL2sXislyrsg%3D%3D
27. S. Hellberg L. Eriksson J. Jonsson F. Lindgren M. Sjöström B. Skagerberg S. Wold and P. Andrews 1991 Int. J. Peptide Protein Res. 37 4141:CAS:528:DyaK38XhsFeguw%3D%3D
28. R. Leardi R. Boggia and M. Terrile 1992 J. Chemometrics 6 26710.1002/ cem.1180060506 1:CAS:528:DyaK3sXhs1ygurY%3D
29. SIMCA-P 8.0. Umetrics UK Ltd., Wokingham Road, RG42 1PL, Bracknell, UK
30. K. Falk O. Rötzschke S. Stefanovic G. Jung and H.-G. Rammensee 1991 Nature, 351 290