A grid-enabled problem solving environment for in-silico screening in drug discovery

Autor: Doman Kim, Sehoon Lee, Jean Salzemann, Jincheol Kim, Hanh Thi Thanh Nguyen, Sangdo Lee, Vincent Breton, Soonwook Hwang

Publikováno v: 5th International Conference on Computer Sciences and Convergence Information Technology.

WISDOM is an international initiative to deploy large-scale in-silico docking on a public grid infrastructure in an attempt to find potential drugs against neglected or emerging diseases such as Malaria and Avian Flu. Within the framework of the WISD

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a6c601974749da5aaef0e5e4d033e1f4
https://doi.org/10.1109/iccit.2010.5711070

The EMBRACE web service collection

Autor: Teresa K. Attwood, Philip McDermott, Steve Pettifer, David G. Pisano, Gert Vriend, Edita Bartaseviciute, Inge Jonassen, Dave Thorne, Jon Ison, Kristoffer Rapacki, Jean Salzemann, Matúš Kalaš, Inb Partners, Vincent Breton, Andrew B. Clegg, Olivier Sand, Mahmut Uludag, Heinz Stockinger, Ali Liaquat, Graham Cameron, Maarten L. Hekkelman, Christophe Blanchet, José M. Fernández, Peter Rice, Erik Bongcam-Rudloff, Jose Manuel Rodriguez

Publikováno v: Nucleic Acids Research, 38, W683-8
Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2010, 38, pp.W683-W688. ⟨10.1093/nar/gkq297⟩
Nucleic acids research, 38 (SUPPL. 2
Nucleic Acids Research, 2010, 38, pp.W683-W688. ⟨10.1093/nar/gkq297⟩
Pettifer, S, Ison, J, Kalas, M, Thorne, D, McDermott, P, Jonassen, I, Liaquat, A, Fernández, J M, Rodriguez, J M, Partners, INB, Pisano, D G, Blanchet, C, Uludag, M, Rice, P, Bartaseviciute, E, Rapacki, K, Hekkelman, M, Sand, O, Stockinger, H, Clegg, A B, Bongcam-Rudloff, E, Salzemann, J, Breton, V, Attwood, T K, Cameron, G & Vriend, G 2010, ' The EMBRACE web service collection ', Nucleic Acids Research, vol. 38, no. Suppl. 2, pp. W683-W688 . https://doi.org/10.1093/nar/gkq297
Nucleic Acids Research, 38, Web Server issue, pp. W683-8

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b59287f413f6df20826e960a6ee1093
http://hdl.handle.net/2066/89021

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Autor: G. Fettahi, Andreas Gisel, K. Mattila, Roberto Fabbretti, Volker Flegel, C. Blanchet, T. Kervinen, Marco Pagni, A.-C. Berglund, Ian J. Tickle, Gert Vriend, Heinz Stockinger, A.L. Da Costa, M. Diarena, Christophe Combet, Eija Korpelainen, V. Bloch, Erik Bongcam-Rudloff, Vincent Breton, Jean Salzemann, Matthieu Reichstadt, Gilbert Deléage, Vinod Kasam, Robbie P. Joosten

Publikováno v: Journal of Applied Crystallography
Journal of Applied Crystallography, International Union of Crystallography, 2009, 42, pp.376-384. ⟨10.1107/S0021889809008784⟩
Journal of Applied Crystallography (International Union of Crystallography-Iucr), 42, 376-385
Journal of applied crystallography (Online) 42 (2009): 376–384. doi:10.1107/S0021889809008784
info:cnr-pdr/source/autori:Gisel, Andreas (6); Stockinger, Heinz (3); Breton, Vincent (2); Mattila, Kimmo (8); Bongcam-Rudloff, Erik (4); Pagni, Marco (3); Joosten, Robbie P. (1); Vriend, Gert (10); Salzemann, Jean (2); Bloch, Vincent (2); Da Costa, Ana L. (2); Diarena, Matteo (2); Fettahi, Géraldine (2); Reichstadt, Matthieu (2); Fabbretti, Roberto (3); Flegel, Volker (3); Berglund, Ann Charlott (4); Blanchet, Christophe (5); Combet, Christophe (5); Deleage, Gilbert (5); Kasam, Vinod (7); Kervinen, Timo (8); Korpelainen, Eija (8); Tickle, Ian J. (9)/titolo:PDB-REDO: Automated re-refinement of X-ray structure models in the PDB/doi:10.1107%2FS0021889809008784/rivista:Journal of applied crystallography (Online)/anno:2009/pagina_da:376/pagina_a:384/intervallo_pagine:376–384/volume:42
Journal of Applied Crystallography (International Union of Crystallography-Iucr), 42, 3, pp. 376-385
Journal of Applied Crystallography, 2009, 42, pp.376-384. ⟨10.1107/S0021889809008784⟩

The majority of previously deposited X-ray structures can be improved by applying current refinement methods.
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c5c5d4caf9c6e0e2b3633193ca09c2d7
http://hal.in2p3.fr/in2p3-00385213

WISDOM-II

Autor: Vincent Breton, Vinod Kasam, Jean Salzemann, N. Jacq

Publikováno v: CLADE@HPDC

After having deployed a first data challenge on malaria and a second one on avian flu, respectively in summer 2005 and spring 2006, we are demonstrating here again how efficiently the computational grids can be used to produce massive docking data at

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::644b7442a6f7b22fb69e9ee27d2f77a2
https://doi.org/10.1145/1273404.1273407

Virtual screening on large scale grids

Autor: Hurng-Chun Lee, Horst Schwichtenberg, Ivan Merelli, Luciano Milanesi, Astrid Maaí, Giulio Rastelli, Vinod Kasam, Martin Hofmann, Vincent Breton, Nicolas Jacq, Yannick Legré, Matthieu Reichstadt, Hsin-Yen Chen, Jean Salzemann, Ying-Ta Wu, Li-Yung Ho, Marc Zimmermann, Emmanuel Medernach, Simon Lin

Publikováno v: Parallel Computing
Parallel Computing, Elsevier, 2007, 33, pp.289-301. ⟨10.1016/j.parco.2007.02.010⟩
Parallel Computing, 2007, 33, pp.289-301. ⟨10.1016/j.parco.2007.02.010⟩
Parallel Computing, Elsevier, 2007, 33, pp.289-301. 〈10.1016/j.parco.2007.02.010〉
HAL Clermont Université
Hyper Article en Ligne
OpenAIRE
INRIA a CCSD electronic archive server
Parallel computing 33 (2007): 289–301. doi:10.1016/j.parco.2007.02.010
info:cnr-pdr/source/autori:Jacq, Nicolas; Breton, Vincent; Chen, Hsin-Yen; Ho, Li-Yung; Hofmann, Martin; Kasam, Vinod; Lee, Hurng-Chun; Legre, Yannick; Lin, Simon C.; Maass, Astrid; Medernach, Emmanuel; Merelli, Ivan; Milanesi, Luciano; Rastelli, Giulio; Reichstadt, Matthieu; Salzemann, Jean; Schwichtenberg, Horst; Wu, Ying-Ta; Zimmermann, Marc/titolo:Virtual screening on large scale grids/doi:10.1016%2Fj.parco.2007.02.010/rivista:Parallel computing/anno:2007/pagina_da:289/pagina_a:301/intervallo_pagine:289–301/volume:33

PCSV, article in press in Parallel Computing; Large scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking withi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e067f12484c450c0170ff7045dce68f9
https://hdl.handle.net/11380/612460