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| Dimitris Dimitropoulos, European Bioinformatics Institute |
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Dimitris Dimitropoulos is a software engineer-chemoinformatician responsible for the PDB ligand dictionary of small molecules in MSD, the European collaborator of wwPDB. He is the developer of the MSD-Chemweb search service for small molecules in the PDB, a popular resource that has been used and referenced extensively in the area in the last few years. As part of this work he has also developed and integrated programs and tools to assist in checking, deriving and publishing ligand-relevant information on the public domain.
Dimitris is one of the architects and developers of the MSDSD relational database that encapsulates the ligand chemistry with all other areas of the PDB and MSD as well as other data sources and public databases. One of the aims of MSDSD where he has significantly contributed is to enable the distribution of the PDB directly in the MSDSD relational database pre-cleaned format. Dimitris has developed methods for incremental and cross-database distribution of MSDSD in Oracle and mySQL.
Finally in order to demonstrate MSDSD, and help users to understand the possibilities of a relational data-warehouse like MSDSD Dimitris developed MSD-mine, a tool for exploring and ad-hoc querying MSDSD over the web that offers functionality for interactive on-line analysis and statistical chart generation. Through drill-down, roll-up functions and aggregation MSD-mine enables users to data-mine all areas of PDB and MSDSD.
Dimitris joined his current position at the Macromolecular Structure Database (MSD) group at the European Bioinformatics Institute (EBI) in 2000 while in the previous 4 yeas to that he worked in the area of very large relational databases and systems for the monitoring, management and optimisation of telecommunication networks. He graduated from the Computer Engineering and Information Technology department of University of Patras-Greece with a five year studies diploma in 1994 and has an MSc in Decision Sciences from University of Hertfordshire-UK.
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Investigating chemical trends in the context of ligand-protein complexes by using on-line data analysis directly on the web
Dimitris Dimitropoulos, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
A prebuild relational data-warehouse with a rich set of relationships for the PDB and the PDB ligands, is the perfect environment for evaluating interesting research questions that may potentially reveal links between ligand chemistry, and the protein environment characteristics. In the MSD search database several common functional groups have been identified for ligands and associated on the atom level to the occurrences of the bound molecules in PDB entries using a consistent nomenclature. These are used as a starting point in order to explore the chemistry relationships to binding site information, secondary structure, and protein classification. As an example we will demonstrate how the MSD-mine tool for on-line data analysis and mining over the web, can be used to examine potential preference of functional fragment distribution towards particular SCOP domains, and in a separate example the contribution of different fragment areas in the binding site activity. The MSD-mine tool and the example scenarios are accessible from http://www.ebi.ac.uk/msdmine.
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