A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease

Bioorganic and Medicinal Chemistry

Volumn 16, Issue 6, 2008, Pages 2903-2911

  Fabry Asztalos, Levente ^a   Andonie, Rǎzvan ^a   Collar, Catharine J ^a   Abdul Wahid, Sarah ^a   Salim, Nicholas ^a  

^a CENTRAL WASHINGTON UNIVERSITY   (United States)

Author keywords

Feature selection; Fuzzy neural network; Genetic algorithm; HIV 1 protease inhibitors; IF THEN rules; QSAR

Indexed keywords

PROTEINASE INHIBITOR;

ACCURACY; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL ACTIVITY; EVOLUTIONARY ALGORITHM; FUZZY SYSTEM; GENETIC ALGORITHM; IC 50; MOLECULAR MODEL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ALGORITHMS; FUZZY LOGIC; HIV PROTEASE; HIV PROTEASE INHIBITORS; HUMANS; INHIBITORY CONCENTRATION 50; LIGANDS; NEURAL NETWORKS (COMPUTER); PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 40949126936     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2007.12.055     Document Type: Article

References (41)

1. Nair A.C., Jayatilleke P., Wang X., Miertus S., and Welsh W.J. J. Med. Chem. 45 (2002) 973-983
2. Jorgensen W.L. Science 303 (2004) 1813-1818
3. Beger R.D., Buzatu D.A., Wilkes J.G., and Lay Jr. J.O. J. Chem. Inf. Comput. Sci. 41 (2001) 1360-1366
4. Suzuki T., Ide K., Ishida M., and Shapiro S. J. Chem. Inf. Comput. Sci. 41 (2001) 718-726
5. Yasri A., and Hartsough D. J. Chem. Inf. Comput. Sci. 41 (2001) 1218-1227
6. Andonie, R.; Fabry-Asztalos, L.; Abdul-Wahid, S.; Collar, C.; Salim, N. Proc. IEEE Int. Conf. Neural Netw., 2006, 7495-7502.
7. Tetko, I. V.; Tanchuk, V. Y.; Luik, A. I. Proceedins of the Seventh Annual IEEE Symposium on Computer Based Medical Systems, 1994, 311-316.
8. Draghici S., and Potter R.B. Bioinformatics 19 (2003) 98-107
9. Weekes D., and Fogel G.B. BioSystems 72 (2003) 149-158
10. Zheng F., Zheng G., Deaciuc A.G., Zhan C.G., Dwoskin L.P., and Crooks P.A. Bioorg. Med. Chem. 15 (2007) 2975-2992
11. Tetko I.V., and Tanchuk V.Y. J. Chem. Inf. Comput. Sci. 42 (2002) 1136-1145
12. Niwa T. J. Chem. Inf. Comput. Sci. 43 (2003) 113-119
13. Yang Z.R., and Thomson R. IEEE Trans. Neural Netw. 16 (2005) 263-274
14. SYBYL Molecular Modeling Software, 7.2 ed.; Tripos Inc.: St. Louis, MO, 2006.
15. BioLoom, Version 2004; BioByte Corp.: Claremont, CA 2004.
16. Ang W.H., Scopelliti R., Bussy F., Juillerat-Jeanneret L., and Dyson P.J. J. Med. Chem. 48 (2005) 8060-8069
17. Peng Y., Keenan S.M., Zhang Q., Kholodovych V., and Welsh W.J. J. Med. Chem. 48 (2005) 1620-1629
18. Andonie, R.; Fabry-Asztalos, L.; Collar, C. J.; Abdul-Wahid, S.; Salim, N. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005, 113-120.
19. Faulon J.L., Visco Jr. D.P., and Pophale R.S. J. Chem. Inf. Comput. Sci. 43 (2003) 707-720
20. Yao X.J., Panaye A., Doucet J.P., Zhang R.S., Chen H.F., Liu M.C., Hu Z.D., and Fan B.T. J. Chem. Inf. Comput. Sci. 44 (2004) 1257-1266
21. Niwa T. J. Med. Chem. 47 (2004) 2645-2650
22. Loukas Y.L. J. Med. Chem. 44 (2001) 2772-2783
23. Tetko I.V., Solov'ev V.P., Antonov A.V., Yao X., Doucet J.P., Fan B., Hoonakker F., Fourches D., Jost P., Lachiche N., and Varnek A. J. Chem. Inf. Model 46 (2006) 808-819
24. Mosier P.D., and Jurs P.C. J. Chem. Inf. Comput. Sci. 42 (2002) 1460-1470
25. Mosier P.D., Counterman A.E., Jurs P.C., and Clemmer D.E. Anal. Chem. 74 (2002) 1360-1370
26. Cecchini M., Kolb P., Majeux N., and Caflisch A. J. Comput. Chem. 25 (2004) 412-422
27. Tetko I.V. J. Chem. Inf. Comput. Sci. 42 (2002) 717-728
28. Tetko I.V., and Bruneau P. J. Pharm. Sci. 93 (2004) 3103-3110
29. Tetko I.V., and Poda G.I. J. Med. Chem. 47 (2004) 5601-5604
30. Tetko I.V., Villa A.E., Aksenova T.I., Zielinski W.L., Brower J., Collantes E.R., and Welsh W.J. J. Chem. Inf. Comput. Sci. 38 (1998) 660-668
31. Senese C.L., and Hopfinger A.J. J. Chem. Inf. Comput. Sci. 43 (2003) 1297-1307
32. Giordanetto F., Cotesta S., Catana C., Trosset J.Y., Vulpetti A., Stouten R.F.W., and Kroemer R.T. J. Chem. Inf. Comput. Sci. 44 (2004) 882-893
33. Boyer F.E., Prasad J.V.N.V., Domagala J.M., Ellsworth E.L., Gaida C., Hagen S.E., Markovski L.J., Tait B.D., Lunney E.A., Palovski A., Ferguson D., Graham N., Holler T., Hupe D., Nouhan C., Tummino P.J., Urumov A., Zeikus G., Gracheck S.J., Sanders J.M., VanderRoest S., Brodfuehrer J., Iyer K., Sinz M., Gulnik S.V., and Erickson J.W. J. Med. Chem. 43 (2000) 843-858
34. Hagen S.E., Domagala J., Gajda C., Lovdahl M., Tait B.D., Wise E., Holler T., Hupe D., Nouhan C., Urumov A., Zeikus G., Zeikus E., Lunney E.A., Pavlovsky A., Gracheck S.J., Saunders J., VanderRoest S., and Brodfuehrer J. J. Med. Chem. 44 (2001) 2319-2332
35. Hagen S.E., Prasad J.V.N.V., Boyer F.E., Domagala J.M., Ellsworth E.L., Gajda C., Hamilton H.W., Markoski L.J., Steinbaugh B.A., Tait B.D., Lunney E.A., Tummino P.J., Ferguson D., Hupe D., Nouhan C., Gracheck S.J., Saunders J.M., and VanderRoest S. J. Med. Chem. 40 (1997) 3707-3711
36. Scholz D., Billich A., Charpiot B., Ettmayer P., Lehr P., Rosenwirth B., Schreiner E., and Gstach H. J. Med. Chem. 37 (1994) 3079-3089
37. Tait B.D., Hagen S., Domagala J., Ellsworth E.L., Gajda C., Hamilton H.W., Prasad J.V.N.V., Ferguson D., Graham N., Hupe D., Nouhan C., Tummino P.J., Humblet C., Lunney E.A., Pavlovsky A., Rubin J., Gracheck S.J., Baldwin E.T., Bhat T.N., Erickson J.W., Gulnik S.V., and Liu B. J. Med. Chem. 40 (1997) 3781-3792
38. Klon A.E., Glick M., and Davies J.W. J. Chem. Inf. Comput. Sci. 44 (2004) 2216-2224
39. Peterson S.D., Schaal W., and Karlen A. J. Chem. Inf. Model 46 (2006) 355-364
40. Cai L.Y., and Kwan H.K. IEEE Trans. Syst. Man Cybern. B 28 (1998) 334-347
41. Siedlecki W., and Sklansky J. Pattern Recognit. Lett. 10 (1989) 335-347