Igemdock: A graphical environment of enhancing gemdock using pharmacological interactions and post-screening analysis

BMC Bioinformatics

Volumn 12, Issue SUPPL. 1, 2011, Pages

  Hsu, Kai Cheng ^a   Chen, Yen Fu ^a   Lin, Shen Rong ^a   Yang, Jinn Moon ^a  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; GRAPHIC ENVIRONMENT; GRAPHICAL ENVIRONMENTS; HIER-ARCHICAL CLUSTERING; INTERACTION PROFILES; PHYSICOCHEMICAL PROPERTY; SCREENING COMPOUNDS; THERAPEUTIC TARGETS;

PROTEINS; LIGANDS;

LIGANDS; BIOINFORMATICS;

PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER PROGRAM; DRUG DEVELOPMENT; INFORMATION RETRIEVAL; PROTEIN BINDING;

BINDING SITES; COMPUTER GRAPHICS; DRUG DISCOVERY; INFORMATION STORAGE AND RETRIEVAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEINS; SOFTWARE;

EID: 79951520837     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S33     Document Type: Article

References (36)

1. Lyne PD. Structure-based virtual screening: an overview. Drug Discovery Today 2002, 7:1047-1055. 10.1016/S1359-6446(02)02483-2, 12546894.
2. Tanrikulu Y, Schneider G. Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening. Nature Reviews Drug Discovery 2008, 7:667-677. 10.1038/nrd2615, 18636071.
3. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Reviews Drug Discovery 2004, 3:935-949. 10.1038/nrd1549, 15520816.
4. Yang J-M, Chen C-C. GEMDOCK: a generic evolutionary method for molecular docking. Proteins 2004, 55:288-304. 10.1002/prot.20035, 15048822.
5. Kramer B, Rarey M, Lengauer T. Evaluation of the flexX incremental construction algorithm for protein-ligand docking. Proteins 1999, 37:228-241. 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8, 10584068.
6. Morris GM, Goodsell DS, Huey R, Olson AJ. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. Journal of Computer-Aided Molecular Design 1996, 10:293-304. 10.1007/BF00124499, 8877701.
7. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology 1997, 267:727-748. 10.1006/jmbi.1996.0897, 9126849.
8. Yang JM, Shen TW. A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators. Proteins 2005, 59(2):205-220. 10.1002/prot.20387, 15726586.
9. Tafi A, Bernardini C, Botta M, Corelli F, Andreini M, Martinelli A, Ortore G, Baraldi PG, Fruttarolo F, Borea PA, et al. Pharmacophore based receptor modeling: the case of adenosine A3 receptor antagonists. An approach to the optimization of protein models. Journal of Medicinal Chemistry 2006, 49:4085-4097. 10.1021/jm051112+, 16821770.
10. Wolber G, Seidel T, Bendix F, Langer T. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug Discovery Today 2008, 13:23-29. 10.1016/j.drudis.2007.09.007, 18190860.
11. Yang JM, Chen YF, Tu YY, Yen KR, Yang YL. Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors. PLoS One 2007, 2:e428. 1855430, 17502914, 10.1371/journal.pone.0000428.
12. Chin KH, Lee YC, Tu ZL, Chen CH, Tseng YH, Yang JM, Ryan RP, McCarthy Y, Dow JM, Wang AH, et al. The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris. Journal of Molecular Biology 2010, 396:646-662. 10.1016/j.jmb.2009.11.076, 20004667.
13. Hung HC, Tseng CP, Yang JM, Ju YW, Tseng SN, Chen YF, Chao YS, Hsieh HP, Shih SR, Hsu JT. Aurintricarboxylic acid inhibits influenza virus neuraminidase. Antiviral Research 2009, 81:123-131. 10.1016/j.antiviral.2008.10.006, 19014974.
14. Yang M-C, Guan H-H, Yang J-M, Ko C-N, Liu M-Y, Lin Y-H, Chen C-J, Mao SJT. Rational design for crystallization of beta-lactoglobulin and vitamin D-3 complex: revealing a secondary binding site. Crystal Growth & Design 2008, 8:4268-4276.
15. Warnmark A, Treuter E, Gustafsson JA, Hubbard RE, Brzozowski AM, Pike AC. Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. Journal of Biological Chemistry 2002, 277:21862-21868. 10.1074/jbc.M200764200, 11937504.
16. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 1998, 95:927-937. 10.1016/S0092-8674(00)81717-1, 9875847.
17. Champness JN, Bennett MS, Wien F, Visse R, Summers WC, Herdewijn P, de Clerq E, Ostrowski T, Jarvest RL, Sanderson MR. Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands. Proteins 1998, 32:350-361. 10.1002/(SICI)1097-0134(19980815)32:3<350::AID-PROT10>3.0.CO;2-8, 9715911.
18. Zhou HB, Sheng S, Compton DR, Kim Y, Joachimiak A, Sharma S, Carlson KE, Katzenellenbogen BS, Nettles KW, Greene GL, et al. Structure-guided optimization of estrogen receptor binding affinity and antagonist potency of pyrazolopyrimidines with basic side chains. Journal of Medicinal Chemistry 2007, 50:399-403. 10.1021/jm061035y, 17228884.
19. Manikowski A, Verri A, Lossani A, Gebhardt BM, Gambino J, Focher F, Spadari S, Wright GE. Inhibition of herpes simplex virus thymidine kinases by 2-phenylamino-6-oxopurines and related compounds: structure-activity relationships and antiherpetic activity in vivo. Journal of Medicinal Chemistry 2005, 48:3919-3929. 1351001, 15916444, 10.1021/jm049059x.
20. Nissink JW, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R. A new test set for validating predictions of protein-ligand interaction. Proteins 2002, 49:457-471. 10.1002/prot.10232, 12402356.
21. Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. Journal of Medicinal Chemistry 2000, 43:4759-4767. 10.1021/jm001044l, 11123984.
22. Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends in Biochemical Sciences 1995, 20:374. 10.1016/S0968-0004(00)89080-5, 7482707.
23. Saldanha AJ. Java Treeview--extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248. 10.1093/bioinformatics/bth349, 15180930.
24. Yang J-M, Shen T-W. A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators. Proteins 2005, 59:205-220. 10.1002/prot.20387, 15726586.
25. Fradera X, Knegtel RM, Mestres J. Similarity-driven flexible ligand docking. Proteins 2000, 40:623-636. 10.1002/1097-0134(20000901)40:4<623::AID-PROT70>3.0.CO;2-I, 10899786.
26. Qin Z, Kastrati I, Chandrasena RE, Liu H, Yao P, Petukhov PA, Bolton JL, Thatcher GR. Benzothiophene selective estrogen receptor modulators with modulated oxidative activity and receptor affinity. Journal of Medicinal Chemistry 2007, 50:2682-2692. 10.1021/jm070079j, 17489582.
27. Manas ES, Xu ZB, Unwalla RJ, Somers WS. Understanding the selectivity of genistein for human estrogen receptor-beta using X-ray crystallography and computational methods. Structure 2004, 12:2197-2207. 10.1016/j.str.2004.09.015, 15576033.
28. Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, Engstrom O, Ohman L, Greene GL, Gustafsson JA, Carlquist M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 1997, 389:753-758. 10.1038/39645, 9338790.
29. Shadnia H, Wright JS, Anderson JM. Interaction force diagrams: new insight into ligand-receptor binding. Journal of Computer-aided Molecular Design 2009, 23:185-194. 10.1007/s10822-008-9250-3, 18989626.
30. Wild K, Bohner T, Folkers G, Schulz GE. The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue. Protein Sci 1997, 6:2097-2106. 2143568, 9336833, 10.1002/pro.5560061005.
31. Kussmann-Gerber S, Kuonen O, Folkers G, Pilger BD, Scapozza L. Drug resistance of herpes simplex virus type 1--structural considerations at the molecular level of the thymidine kinase. European Journal of Biochemistry / FEBS 1998, 255:472-481. 10.1046/j.1432-1327.1998.2550472.x, 9716390.
32. Hinds TA, Compadre C, Hurlburt BK, Drake RR. Conservative mutations of glutamine-125 in herpes simplex virus type 1 thymidine kinase result in a ganciclovir kinase with minimal deoxypyrimidine kinase activities. Biochemistry 2000, 39:4105-4111. 10.1021/bi992453q, 10747801.
33. Pilger BD, Perozzo R, Alber F, Wurth C, Folkers G, Scapozza L. Substrate diversity of herpes simplex virus thymidine kinase. Impact Of the kinematics of the enzyme. The Journal of Biological Chemistry 1999, 274:31967-31973. 10.1074/jbc.274.45.31967, 10542226.
34. Evans JS, Lock KP, Levine BA, Champness JN, Sanderson MR, Summers WC, McLeish PJ, Buchan A. Herpesviral thymidine kinases: laxity and resistance by design. The Journal of General Virology 1998, 79:2083-2092.
35. Pan Y, Huang N, Cho S, MacKerell AD. Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inf Comput Sci 2003, 43(1):267-272.
36. Sulpizi M, Schelling P, Folkers G, Carloni P, Scapozza L. The rational of catalytic activity of herpes simplex virus thymidine kinase. a combined biochemical and quantum chemical study. The Journal of Biological Chemistry 2001, 276:21692-21697.