Abstract
The rapid progress of biotechnology provides an increasing number of life science databases. These databases have been operated and managed individually on the Internet. Under such a circumstance, it is needed to develop an infrastructure that allows to share information contained in these databases and to conduct research collaboration. Grid technology is an emerging technology for seamless and loose integration of diverse resources distributed on the Internet. In order to achieve federation of the heterogeneous databases, we have developed a system for supporting a drug discovery process using Globus Toolkit3/OGSA-DAI. As an essential part of the system, we introduce a protein-compound interaction search based on a meta-data bridging protein and compound information with their interaction types; such as, inhibitor, agonist, antagonist, etc. The effectiveness of our system is demonstrated by searching for the candidate compounds interacting with the glucocorticoid receptor protein.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Nakamura, H., Date, S., Matsuda, H., Shimojo, S.: A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. New Generation Computing 22, 157–166 (2004)
Foster, I., Kesselman, C., Nick, J., Tuecke, S.: The Physiology of the Grid. An Open Grid Services Architecture for Distributed Systems Integration. Open Grid Service Infrastructure WG, Global Grid Forum (2002), http://www.ggf.org/
Global Grid Forum, http://www.gridforum.org/
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O’Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research 31, 365–370 (2003)
Wu, C.H., Yeh, L.S., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., Hu, Z., Kourtesis, P., Ledley, R.S., Suzek, B.E., Vinayaka, C.R., Zhang, J., Barker, W.C.: The Protein Information Resource. Nucleic Acids Research 31, 345–347 (2003)
Bourne, P.E., Addess, K.J., Bluhm, W.F., Chen, L., Deshpande, N., Feng, Z., Fleri, W., Green, R., Merino-Ott, J.C., Townsend-Merino, W., Weissig, H., Westbrook, J., Berman, H.M.: The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Research 32(Database issue), D223–D225 (2004)
OGSA-DAI Project, http://www.ogsadai.org
UK e-Science (GRID) core programme, http://www.escience-grid.org.uk/
Kosaka, T., Tohsato, Y., Date, S., Hatsuda, H., Shimojo, S.: An OGSA-Based Integration of Life Scientific Resources toward Drug Discovery. In: Proc. of HealthGRID 2004, Clermont-Ferrand (2004) (in press)
Schuffenhauer, A., Zimmermann, J., Stoop, R., van der Vyver, J.J., Lecchini, S., Jacoby, E.: An ontology for pharmaceutical ligands and its application for in silico screening and library design. Journal of Information and Computer Sciences 42, 947–955 (2002)
Schuffenhauer, A., Floersheim, P., Acklin, P., Jacoby, E.: Similarity metrics for ligands reflecting the similarity of the target proteins. Journal of Information and Computer Sciences 43, 391–405 (2003)
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389–3402 (1997)
Xu, J.: GMA: A Generic Match Algorithm for structural Homomorphism, Isomorphism, Maximal Common Substructure Match and Its Applications. Journal of Chemical Information and Computer Sciences 36, 25–34 (1996)
Flower, D.R.: On the Properties of Bit String-Based Measures of Chemical Similarity. Journal of Chemical Information and Computer Sciences 38, 379–386 (1998)
MDL Drug Data Report Version (2003) 2, MDL ISIS/HOST software, MDL Information Systems, Inc. San Leandro, CA (2003), http://www.mdl.com
Brown, R.D., Martin, Y.C.: Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. Journal of Information and Computer Sciences 36, 572–584 (1996)
Xue, L., Godden, J.W., Bajorath, J.: Database Searching for Compounds with Similar Biological Activity Using Short Binary Bit String Representations of Molecules. Journal of Chemical Information and Computer Sciences 39, 881–886 (1996)
Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.: UniProt: the Universal Protein Knowledgebase. Nucleic Acids Research 32(Database issue), D115–D119 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Tohsato, Y., Kosaka, T., Date, S., Shimojo, S., Matsuda, H. (2005). Heterogeneous Database Federation Using Grid Technology for Drug Discovery Process. In: Konagaya, A., Satou, K. (eds) Grid Computing in Life Science. LSGRID 2004. Lecture Notes in Computer Science(), vol 3370. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32251-1_5
Download citation
DOI: https://doi.org/10.1007/978-3-540-32251-1_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25208-5
Online ISBN: 978-3-540-32251-1
eBook Packages: Computer ScienceComputer Science (R0)