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RESEARCH
[ CNB ]

[ CSIC ]
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Development of new databases

Current Projects

Construction of the FEMME Database

The goal of this work is the automatic identification and characterisation of the channels and cavities from medium resolution data solved by 3D-EM.

In order to identify channels and cavities we have extended the mathematical theory of alpha complex (Edelsbrunner H et al 1994) from its previous application to atomic resolution data (Liang J et al 1998) to intermediate resolution data with good results. To this end we have also extended our newly derived quantization algoritms (Pascual-Montano et al 2001) to be able to extract from the medium resolution data, a set of "pseudo atoms" guiding points (De-Alarcón P.A in press).

We have stored the extracted channels/cavities of our set of macromolecules at different resolutions together with its features, the low resolution representation and relevant information about the function of the whole macromolecule in the FEMME database (Feature Extraction in a Multiresolution Macromolecular Environment). At the moment this database is in the test phase only storing information about a reduced set of macromolecules in XML files. The non-existence of a database to organise the 3D-EM structural data has forced us to do this process in a manual way, individually selecting a set of suitable structures. This situation is expected to change in the nearby future assigning this kind of feature extraction to a multiresolution database. Thus the following objective is the automation of the process that will allow us to enlarge our database to the whole set of structures solved by the different techniques independently of the resolution ( IIMS project ). At that moment we will be able to do functional extrapolations among the data stored in FEMME in the sense that we will interpret a similarity in channels or cavities as a possible similarity in function and this could give us some clues in the characterisation of a not very well known macromolecule. Another important feature of our database is that we can query for a macromolecule channel or cavity independently of the technique employed to solve it. Thus, the FEMME database will provide us with important information about not only conventional channels and cavities but also the ones formed by the association of several subunits that only can be seen through medium resolution techniques (3D-EM). FEMME database will also supply the user with all the necessary tools to compare a newly solved structure (or the channels/cavities on it) with all the structures stored in it.

In conclusion, the final aim of this study is the extraction of some important clues referring to the structure-function relationships and the observation of channels/cavities variations with the resolution.

Funded in part by European Community Contract No. QLRI-CT-2001-00015 for "TEMBLOR" under the specific RTD programme "Quality of Life and Management of Living Resources"

Integration of Information about Macromolecular Structure (IIMS)

Our overall goal is to develop a system to integrate the results of three-dimensional electron microscopy (3D-EM) with models from X-ray and NMR methods. The integration of the data of the three major experimental techniques of three-dimensional structural determination into a single standardised data base will be publically available from the central European biological data base service provider, the European Bioinformatics Institute (EBI) .

More information about the IIMS project can be found in the IIMS official web site at the EBI.

IIMS participants:

Funded by European Community contract-no. QLRI-CT-2000-31237 under the RTD programme "Quality of Life and Management of Living Resources"

Modelling and searching for structural information

Our final aim is to provide the capability of querying a database of 3D datasets by using the intrisic geometric content of the macromolecule rather than simple text or annotations on it. Thus, this research is focused on the development of data models able to capture and represent the geometric features of a 3D macromolecule. Also directional as well as topological relationships among interesting components need to be modeled. To this end, special algorithms (and the corresponding distance measures) are being developed in order to extract geometric descriptors for shape, size and so on.

More detailed description of this work.

Funded in part by European Community Contract No. QLRI-CT-2001-00015 for "TEMBLOR" under the specific RTD programme "Quality of Life and Management of Living Resources"

Previous Projects:

BioImage (Dec. 1996- Dec. 1999)

The work carried out during the BioImage Project has resulted in the first implementation of a database of multidimensional biological images obtained by various microscopy techniques.

The BioImage database scope is rather broad, addressing three-dimensional biological information which spans several orders of magnitude, from macromolecules to entire cells and organisms.