WFReDoW: A cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model

BioMed Research International

Volumn 2013, Issue , 2013, Pages

  De Paris, Renata ^a   Frantz, Fábio A ^a   Norberto De Souza, Osmar ^a   Ruiz, Duncan D A ^a  

^a PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; FULLY FLEXIBLE RECEPTOR MODEL; INTERNET; MATHEMATICAL MODEL; MOLECULAR DOCKING; MYCOBACTERIUM TUBERCULOSIS; WORKFLOW; ALGORITHM; CHEMISTRY; ENZYMOLOGY;

BACTERIAL PROTEIN; CELL SURFACE RECEPTOR; INHA PROTEIN, MYCOBACTERIUM; OXIDOREDUCTASE;

ALGORITHMS; BACTERIAL PROTEINS; INTERNET; MOLECULAR DOCKING SIMULATION; MYCOBACTERIUM TUBERCULOSIS; OXIDOREDUCTASES; RECEPTORS, CELL SURFACE;

EID: 84877277360     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2013/469363     Document Type: Article

References (27)

1. Luscombe N. M., Greenbaum D., Gerstein M., What is bioinformatics? A proposed definition and overview of the field. Methods of Information in Medicine 2001 40 4 346 358 2-s2.0-0034868592 (Pubitemid 32803300)
2. Kuntz I. D., Structure-based strategies for drug design and discovery. Science 1992 257 5073 1078 1082 2-s2.0-0026730489
3. Kapetanovic I. M., Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chemico-Biological Interactions 2008 171 2 165 176 2-s2.0-38549117345 10.1016/j.cbi.2006.12.006 (Pubitemid 351146652)
4. Wei B. Q., Weaver L. H., Ferrari A. M., Matthews B. W., Shoichet B. K., Testing a flexible-receptor docking algorithm in a model binding site. Journal of Molecular Biology 2004 337 5 1161 1182 2-s2.0-1842471241 10.1016/j.jmb.2004. 02.015 (Pubitemid 38445058)
5. Morris G. M., Huey R., Lindstrom W., Sanner M. F., Belew R. K., Goodsell D. S., Olson A. J., Software news and updates AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. Journal of Computational Chemistry 2009 30 16 2785 2791 2-s2.0-70349932423 10.1002/jcc.21256
6. Machado K. S., Winck A. T., Ruiz D. D. A., Norberto de Souza O., Mining flexible-receptor docking experiments to select promising protein receptor snapshots. BMC Genomics 2010 11 supplement 5, article S6 2-s2.0-78650813408 10.1186/1471-2164-11-S5-S6
7. Machado K. S., Wick A. T., Ruiz D. D. A., Norberto de Souza O., Mining flexible-receptor molecular docking data. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery 2011 1 6 532 541 10.1002/widm.46
8. Lin J. H., Perryman A. L., Schames J. R., McCammon J. A., The relaxed complex method: accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003 68 1 47 62 2-s2.0-0037231646 10.1002/bip.10218 (Pubitemid 36098307)
9. Alonso H., Bliznyuk A. A., Gready J. E., Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews 2006 26 531 568 (Pubitemid 44230412)
10. Hübler P., P-SaMI: self-adapting multiple instances-a data pattern to scientific workflows (in portuguese: P-SaMI: padrão de múltiplas instâncias autoadaptáveis-um padrão de dados para workflows científicos) [Ph.D. thesis] 2010 Porto Alegre, Brasil PPGCC-PUCRS
11. De Paris R., Frantz F. A., Norberto de Souza O., Ruiz D. D. A., A conceptual many tasks computing architecture to execute molecular docking simulations of a fully-flexible receptor model. Advances in Bioinformatics and Computational Biology 2011 6832 75 78
12. Jiang X., Kumar K., Hu X., Wallqvist A., Reifman J., DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chemistry Central Journal 2008 2 article 18 2-s2.0-52249109585 10.1186/1752-153X-2-18
13. Prakhov N. D., Chernorudskiy A. L., Gainullin M. R., VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters. Bioinformatics 2010 26 10 1374 1375 2-s2.0-77952832378 10.1093/bioinformatics/btq149
14. Abreu R. M. V., Froufe H. J. C., Queiroz M. J. R. P., Ferreira I. C. F. R., MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters. Journal of Cheminformatics 2010 2 1, article 10 2-s2.0-78649692457 10.1186/1758-2946-2-10
15. Collignon B., Schulz R., Smith J. C., Baudry J., Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. Journal of Computational Chemistry 2011 32 6 1202 1209 2-s2.0-79952528590 10.1002/jcc.21696
16. Norgan A. P., Coffman P. K., Kocher J. A., Katzman K. J., Sosa C. P., Multilevel parallelization of AutoDock 4.2. Journal of Cheminformatics 2011 3 1 7
17. Ellingson S. R., Baudry J., High-throughput virtual molecular docking with AutoDockCloud. Concurrency and Computation: Practice and Experience 2012 10.1002/cpe.2926
18. Amazon elastic compute cloud. http://aws.amazon.com/ec2/
19. Irwin J. J., Shoichet B. K., ZINC-a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling 2005 45 1 177 182 2-s2.0-13844312649 10.1021/ci049714+ (Pubitemid 40736970)
20. Kuo M. R., Morbidoni H. R., Alland D., Sneddon S. F., Gourlie B. B., Staveski M. M., Leonard M., Gregory J. S., Janjigian A. D., Yee C., Musser J. M., Kreiswirth B., Iwamoto H., Perozzo R., Jacobs W. R., Sacchettini J. C., Fidock D. A., Targeting tuberculosis and malaria through inhibition of enoyl reductase: compound activity and structural data. Journal of Biological Chemistry 2003 278 23 20851 20859 2-s2.0-0038757566 10.1074/jbc.M211968200 (Pubitemid 36806391)
21. Schroeder E. K., Basso L. A., Santos D. S., De Souza O. N., Molecular dynamics simulation studies of the wild-type, I21V, and I16T mutants of isoniazid-resistant Mycobacterium tuberculosis enoyl reductase (InhA) in complex with NADH: toward the understanding of NADH-InhA different affinities. Biophysical Journal 2005 89 2 876 884 2-s2.0-23244433410 10.1529/biophysj.104. 053512 (Pubitemid 41098974)
22. Buyya R., Yeo C. S., Venugopal S., Broberg J., Brandic I., Cloud computing and emerging IT platforms: vision, hype, and reality for delivering computing as the 5th utility. Future Generation Computer Systems 2009 25 6 599 616 2-s2.0-63649117166 10.1016/j.future.2008.12.001
23. Banino C., Beaumont O., Carter L., Ferrante J., Legrand A., Robert Y., Scheduling strategies for master-slave tasking on heterogeneous processor platforms. IEEE Transactions on Parallel and Distributed Systems 2004 15 4 319 330 2-s2.0-1942436288 10.1109/TPDS.2004.1271181
24. Machado K. S., Schroeder E. K., Ruiz D. D., Cohen E. M. L., Norberto de Souza O., FReDoWS: a method to automate molecular dockings simulations with explicit receptor flexibility and snapshots selection. BMC Genomics 2011 12 2 13
25. Raicu I., Foster I., Wilde M., Zhang Z., Iskra K., Beckman P., Zhao Y., Szalay A., Choudhary A., Little P., Moretti C., Chaudhary A., Thain D., Middleware support for many-task computing. Cluster Computing 2010 13 291 314
26. Winck A. T., MacHado K. S., Norberto de Souza O., Ruiz D. D., FReDD: supporting mining strategies through a flexible-receptor docking database. Advances in Bioinformatics and Computational Biology 2009 5676 143 146 2-s2.0-69949120570 10.1007/978-3-642-03223-3-13
27. Rabenseifner R., Hager G., Jost G., Hybrid MPI/OpenMP parallel programming on clusters of multi-core SMP nodes. Proceedings of the 17th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP '09) February 2009 Weimar, Germany IEEE Press 427 436 2-s2.0-70349124617 10.1109/PDP.2009.43