IScreen: World's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 6, 2011, Pages 525-531

  Tsai, Tsung Ying ^a   Chang, Kai Wei ^a   Chen, Calvin Yu Chian ^a,b,c  

^a CHINA MEDICAL UNIVERSITY   (Taiwan)

^b HARVARD MEDICAL SCHOOL   (United States)

^c Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Cloud computing; De novo; Docking; Screening; Traditional Chinese medicine (TCM)

Indexed keywords

CLOUD COMPUTING; DIAGNOSIS; PROTEINS; WEB SERVICES;

CLOUD-COMPUTING; DE NOVO; DOCKING; DRUG DESIGN; INTELLIGENT SCREENINGS; SCREENING SYSTEM; TRADITIONAL CHINESE MEDICINE; VIRTUAL SCREENING; WEB SERVERS;

DATABASE SYSTEMS;

ALGORITHM; ARTICLE; CHINESE MEDICINE; COMPUTER AIDED DESIGN; COMPUTER INTERFACE; DATA ANALYSIS SOFTWARE; DATA BASE; DRUG DESIGN; DRUG INDUSTRY; MOLECULAR DOCKING; PH; PRIORITY JOURNAL; TAIWAN; VIRTUAL REALITY; WEB BROWSER;

EID: 80051545693     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9438-9     Document Type: Article

References (37)

1. CY Chen CYC Chen 2010 Insights into designing the dual-targeted HER2/HSP90 inhibitors J Mol Graphics Model 29 1 21 31 10.1016/j.jmgm.2010.04.002
2. TT Chang HJ Huang KJ Lee HW Yu HY Chen FJ Tsai MF Sun CY Chen 2010 Key features for designing phosphodiesterase-5 inhibitors J Biomol Struct Dyn 28 3 309 321 1:CAS:528:DC%2BC3cXht12isbbK
3. CY Chen HJ Huang FJ Tsai CYC Chen 2010 Drug design for Influenza A virus subtype H1N1 J Taiwan Inst Chem Eng 41 1 8 15 10.1016/j.jtice.2009.06.007 1:CAS:528:DC%2BC3cXktVOrurc%3D
4. CYC Chen 2010 Virtual screening and drug design for PDE-5 receptor from traditional chinese medicine database J Biomol Struct Dyn 27 5 627 640 1:CAS:528:DC%2BC3cXhvV2is7w%3D
5. CYC Chen 2009 Chemoinformatics and pharmacoinformatics approach for exploring the GABA-A agonist from Chinese herb suanzaoren J Taiwan Inst Chem Eng 40 1 36 47 10.1016/j.jtice.2008.07.011 1:CAS:528:DC%2BD1MXhsVymtb8%3D
6. CYC Chen 2007 Computational screening and design of traditional Chinese medicine (TCM) to block phosphodiesterase-5 J Mol Graphics Model 28 4 261 269
7. KC Chen CYC Chen 2011 Stroke Prevention by traditional Chinese medicine? A genetic algorithm, support vector machine and molecular dynamics approach Soft Matter 7 8 4001 4008 10.1039/c0sm01548b 1:CAS:528:DC%2BC3MXkt1Kjs7w%3D
8. CYC Chen 2011 TCM Database@Taiwan: the world's largest traditional chinese medicine database for drug screening in silico PLoS One 6 1 e15939 10.1371/journal.pone.0015939 1:CAS:528:DC%2BC3MXosVynug%3D%3D
9. O Korb T Stutzle TE Exner 2009 Empirical scoring functions for advanced protein-ligand docking with PLANTS J Chem Inf Model 49 1 84 96 10.1021/ci800298z 1:CAS:528:DC%2BD1MXisVSquw%3D%3D
10. G Jones P Willett RC Glen 1995 Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J Mol Biol 245 1 43 53 10.1016/S0022-2836(95)80037-9 1:CAS:528:DyaK2MXjtVKlsbc%3D
11. G Jones P Willett RC Glen AR Leach R Taylor 1997 Development and validation of a genetic algorithm for flexible docking J Mol Biol 267 3 727 748 10.1006/jmbi.1996.0897 1:CAS:528:DyaK2sXis1KntLo%3D (Pubitemid 27170693)
12. JJ Irwin BK Shoichet MM Mysinger N Huang F Colizzi P Wassam Y Cao 2009 Automated docking screens: a feasibility study J Med Chem 52 18 5712 5720 10.1021/jm9006966 1:CAS:528:DC%2BD1MXhtVOjurjN
13. D Douguet H Munier-Lehmann G Labesse S Pochet 2005 LEA3D: a computer-aided ligand design for structure-based drug design J Med Chem 48 7 2457 2468 10.1021/jm0492296 1:CAS:528:DC%2BD2MXhs1yku7c%3D (Pubitemid 40516437)
14. MN Wass LA Kelley MJ Sternberg 2010 3DLigandSite: predicting ligand-binding sites using similar structures Nucleic Acids Res 38 Web Server issue W469 W473 10.1093/nar/gkq406 1:CAS:528:DC%2BC3cXotVSqtro%3D
15. X Liu S Ouyang B Yu Y Liu K Huang J Gong S Zheng Z Li H Li H Jiang 2010 PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach Nucleic Acids Res 38 Web Server issue W609 W614 10.1093/nar/gkq300 1:CAS:528:DC%2BC3cXotVWjsL4%3D
16. F Dey A Caflisch 2008 Fragment-based de novo ligand design by multiobjective evolutionary optimization J Chem Inf Model 48 3 679 690 10.1021/ci700424b 1:CAS:528:DC%2BD1cXisFWltbc%3D (Pubitemid 351535435)
17. JMS Law DYK Fung Z Zsoldos A Simon Z Szabo IG Csizmadia AP Johnson 2003 Validation of the SPROUT de novo design program Theochem-J Mol Struct 666 651 657 10.1016/j.theochem.2003.08.104
18. DJ Danziger PM Dean 1989 Automated site-directed drug design: the prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces Proc R Soc Lond B Biol Sci 236 1283 115 124 10.1098/rspb.1989.0016 1:CAS:528:DyaL1MXktVSisr4%3D (Pubitemid 19085345)
19. Y Nishibata A Itai 1993 Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation J Med Chem 36 20 2921 2928 10.1021/jm00072a011 1:CAS:528:DyaK3sXlslelsrw%3D (Pubitemid 23315395)
20. CW Murray DE Clark DG Byrne 1995 PRO-LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides J Comput-Aided Mol Des 9 5 381 395 10.1007/BF00123996 1:CAS:528:DyaK2MXpslehsro%3D
21. SH Rotstein MA Murcko 1993 GenStar: a method for de novo drug design J Comput-Aided Mol Des 7 1 23 43 10.1007/BF00141573 1:CAS:528:DyaK3sXktVShur4%3D
22. HJ Bohm 1992 The computer program LUDI: a new method for the de novo design of enzyme inhibitors J Comput-Aided Mol Des 6 1 61 78 10.1007/BF00124387 1:STN:280:DyaK383mtVarsw%3D%3D
23. DC Roe ID Kuntz 1995 BUILDER v.2: improving the chemistry of a de novo design strategy J Comput-Aided Mol Des 9 3 269 282 10.1007/BF00124457 1:CAS:528:DyaK2MXntFGksrk%3D
24. DA Pearlman MA Murcko 1996 CONCERTS: dynamic connection of fragments as an approach to de novo ligand design J Med Chem 39 8 1651 1663 10.1021/jm950792l 1:CAS:528:DyaK28XhslGqsr4%3D (Pubitemid 26120068)
25. HM Vinkers MR de Jonge FF Daeyaert J Heeres LM Koymans JH van Lenthe PJ Lewi H Timmerman K Van Aken PA Janssen 2003 SYNOPSIS: synthesize and optimize system in silico J Med Chem 46 13 2765 2773 10.1021/jm030809x 1:CAS:528:DC%2BD3sXjvFOiurc%3D (Pubitemid 36702544)
26. N Brown B McKay F Gilardoni J Gasteiger 2004 A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules J Chem Inf Comput Sci 44 3 1079 1087 1:CAS:528:DC%2BD2cXjs1ens7Y%3D
27. Chen G, Li S (1992) Ben cao gang mu tong shi = general explanation of compendium of materia medica. Xue yuan chu ban she, Beijing Shi
28. Fang Y, Zhang Z, Miao X (1991) Shang han lun tiao bian, Shanghai gu ji chu ban she : Xin hua shu dian Shanghai fa xing suo fa xing, Shanghai
29. Lü X (2002) Zhong yao jian bie da quan. Hunan ke xue ji shu chu ban she, Changsha Shi
30. Miao X, Zheng J (2002) Shennong ben cao jing shu. Zhong yi gu ji chu ban she, Beijing
31. Nanjing Zhong yi yao da xue, Zhao G, Dai S, Chen R (2006) Zhong yao da ci dian. Shanghai ke xue ji shu chu ban she, Shanghai
32. EW Sayers T Barrett DA Benson E Bolton SH Bryant K Canese V Chetvernin DM Church M DiCuccio S Federhen M Feolo LY Geer W Helmberg Y Kapustin D Landsman DJ Lipman ZY Lu TL Madden T Madej DR Maglott A Marchler-Bauer V Miller I Mizrachi J Ostell A Panchenko KD Pruitt GD Schuler E Sequeira ST Sherry M Shumway K Sirotkin D Slotta A Souvorov G Starchenko TA Tatusova L Wagner YL Wang WJ Wilbur E Yaschenko J Ye 2010 Database resources of the National Center for Biotechnology Information Nucleic Acids Res 38 D5 D16 10.1093/nar/gkp967 1:CAS:528:DC%2BC3cXktlOrtQ%3D%3D
33. M Clark 1998 The ISI web of science Abstracts of Papers of the American Chemical Society 216 U525
34. T Gunda 2007 ChemBioOffice Chem World 4 11 70
35. Y Karzazi G Surpateanu 1999 An empirical MM2 augmented force field for the cycloimmonium ylides J Mol Struct 510 1-3 197 205 10.1016/S0022-2860(99) 00079-4 1:CAS:528:DyaK1MXntFWltLg%3D (Pubitemid 29529737)
36. CA Lipinski F Lombardo BW Dominy PJ Feeney 2001 Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv Drug Del Rev 46 1-3 3 26 10.1016/S0169-409X(00)00129-0 1:CAS:528:DC%2BD3MXitVOhs7o%3D (Pubitemid 33653411)
37. JC Gordon JB Myers T Folta V Shoja LS Heath A Onufriev 2005 H ++: a server for estimating pKas and adding missing hydrogens to macromolecules Nucleic Acids Res 33 Web Server issue W368 W371 10.1093/nar/gki464 1:CAS:528:DC%2BD2MXlslyqt7k%3D (Pubitemid 44529945)