LAB PRESENTATION : The Research Unit in Biomedical Informatics (GRIB), Barcelona

The Research Unit on Biomedical Informatics (GRIB, www.imim.es/grib) is a joint research unit of IMIM-Hospital del Mar (www.imim.es) and Universitat Pompeu Fabra (UPF, www.upf.edu). It was created by Prof. Ferran Sanz in 1985. This unit carries out methodological research and technological developments on the application of advanced information technologies and computational methods in the health and life sciences, with a particular focus in pharmaceutical R&D. The GRIB brings together a team of more than sixty scientists, as well as technical and management staff. GRIB has a wide experience in the participation and coordination of research projects funded by the European Commission. In the last years, the unit has participated in more than 20 European projects. The GRIB is also involved in a significant number of other research projects funded in competitive calls. On the other hand, it has a long tradition of collaboration with the industry in the framework of R&D projects. GRIB staff is involved in pre and postgraduate teaching at the UPF, with a particularly intense involvement in its master degree in Bioinformatics in Health Sciences (diana.imim.es/Bioinformatics).

The GRIB is currently organised in seven laboratories:

  • Computational Genomics (Mar Albà, Eduardo Eyras, Núria Lòpez-Bigas, Robert Castelo) is devoted to the computational analysis of genomic sequences and information. Roderic Guigó, director of the Bioinformatics Programme of the Centre for Genomic Regulation (CRG) acts as stable consultant of this lab.
  • Complex Systems (Ricard V. Solé), a lab devoted to the understanding and modelling of complex biosystems, their synthesis and evolution.
  • Structural Bioinformatics (Baldomero Oliva) dedicated to the analysis and modelling of protein 3D structures, as well as these of macromolecular interactions.
  • Computational Biochemistry and Biophysics (Jordi Villà-Freixa, Gianni de Fabritiis), which is devoted to the development and use of modelling and simulation methods to understand biochemical and biophysical phenomena at the molecular and systemic levels.
  • Chemogenomics (Jordi Mestres), which is dedicated to the development of novel integrative bio-chemoinformatics methods and its application to the annotation of large chemical libraries to entire protein families of therapeutic interest.
  • Computer-Assisted Drug Design (Manuel Pastor), a group focused on the development and application of computational methods oriented to the discovery and development of new drugs. Ismael Zamora, Director of Lead Molecular Design, is a part-time member of this group.
  • Integrative Biomedical Informatics (Ferran Sanz), a singular group particularly dedicated to the generation and execution of research initiatives that aim to contribute to the solution of biomedical problems on the basis of the join application of methods and strategies afforded in different GRIB labs.

Some examples of methods and tools developed at the GRIB in the field of pharmacoinformatics are the SHED descriptors (1), as well as the GRIND ones developed in collaboration with Molecular Design Ltd. (2). Regarding recent applications of these methods in the Medicinal Chemistry field, GRIB scientists have recently published papers on chemoinformatic studies of antipsychotics (3), as well as a chemogenomic profiling of nuclear receptors (4). On the other hand, the GRIB is currently participating in the CancerGrid and ALERT EU-funded projects within the pharmaceutical field, as well as in the EUROPIN initiative for establishing a European doctorate in Pharmacoinformatics.

The research activity of GRIB has originated the creation of two spin-off companies: Pharmatools Interactive Services, promoted by Ferran Sanz, and Chemotargets, promoted by Jordi Mestres. Finally, it has to be pointed out that GRIB is the node for Biomedical Informatics of the Spanish Institute of Bioinformatics (INB).

By Gerhard F. Ecker, University of Vienna

_______________________________________________________

References

(1) Gregori-Puigjané E, Mestres J. SHED: Shannon entropy descriptors from topological feature distributions. J Chem Inf Model 2006; 46(4):1615-22.
(2) Fontaine F, Pastor M, Sanz F. Incorporating molecular shape into the alignment-free Grid-Independent Descriptors. J Med Chem 2004; 47(11): 2805-15.
(3) Dezi C, Brea J, Alvarado M, Raviña E, Masaguer CF, Loza MI, Sanz F, Pastor M. Multistructure 3D-QSAR studies on a series of conformationally constrained butyrophenones docked into a new homology model of the 5-HT2A receptor. J Med Chem 2007; 50(14): 3242-55.
(4) Hettne K, Cases M, Boyer S, Mestres J. Connecting small molecules to nuclear receptor pathways. Curr Top Med Chem 2007; 7(15):1530-6.




Figure 1


Figure 2: Docking of butyrophenones in the h5HT2AR model (taken from Ref 3)

Editor

Gerhard Ecker
Univ. Vienna, AT

Editorial Committee

Koen Augustyns
Univ. Antwerpen, BE

Erden Banoglu
Gazi Univ., TR

Gabriele Costantino
Univ. Parma, IT

Jordi Mestres
IMIM-UPF, ES

Kristian Stromgaard
Univ. Copenhagen, DK

Executive Committee

Roberto Pellicciari President
Gerhard F.Ecker Pres. Elect
Rasmus P.Clausen Secr/Treas
David Alker Member
Brigitte Lesur Member
Peter Matuys Member

For more information please contact info@efmc.info