Research groups

Structural BioInformatics group of GRIB

Protein-protein interactions play a relevant role among the different functions of a cell. Identifying the protein-protein interaction network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. A paradox in protein-protein binding is to explain how the unbound proteins of a binary complex recognize each other among a large population within a cell and how they find their best docking interface in a short time-scale. Our group interrogate protein structure to unveil its function, generate the network of interactions and to relate genes/proteins with diseases by means of exploiting the topology of the network. 

Our expertises are on

  • the study of the relationship between sequence, structure and function of proteins: Characterization of the structural motifs involved in the function and interactions between proteins. Development of statistical potentials and analysis of physico-chemical potentials helping to describe the fold and function of proteins and its interactions with other macro-molecules.
  • the prediction of protein-protein and protein-DNA interactions: Structural analysis of docking approaches and development of new techniques towards the prediction of binding sites and the mechanisms of interface selection of protein-protein and protein-DNA interactions.
  • the analysis of protein interaction networks and its use on bio-medicine, helping to detect potential targets and prioritization of candidate disease-genes. Development of methods to study and integrate information for different types of networks and application on the study of metastasis. Prediction of signalling networks, such as the phosphorylation network and other post-transcriptional modifications, and integration with genomic data, such as microarrays.

The Structural BioInformatics group of GRIB led by Baldo Oliva is integrated in the Research Programme on Biomedical Informatics, GRIB. The GRIB is a joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra. The GRIB mission is to develop and apply computational methods and information technologies for a better understanding and prediction of biological phenomena, giving especial emphasis to those related to the human diseases, their prevention, diagnosis and pharmacological treatment.   

Main projects

  • 1.

    Development of Bioinformatic tools to study the mechanisms of protein-interaction network rewiring: application in systems medicine

    This project is based in: i) the analysis of the interface of known and modelled structures of protein-protein interactions (PPIs) to predict the strength of the interaction; and ii) the analysis of changes in regions outside the interface of a PPI that modify its prediction. We study if changes in sequence (or conformation) can disrupt an interaction and modify the protein interaction network (PIN). Our final goal is to provide the tools helping researchers to analyze and predict the conditional rewiring of a PIN, caused by changes in the sequence or conformation of its proteins. This project BIO2014-57518 PINR-sysmed is funded by the MINECO.

  • 2.

    Integration, analisis and model of biological pathways: scoring functions for bio-molecular interactions and genome wide association studies (GWAS)

    Project reference BIO2011-22568 funded by MINECO & FEDER

  • 3.

    ERASysBio: Living with uninvited guests-comparing plant and animal responses to endocytic invasions

    Project reference EUI2009-04018 funded by MINECO, EC & FEDER

Website

Institutions

Bioinformatics expertise:

Group Leader:

Baldo Oliva

PI

Contact:

Chus Donlo

Bioinformatics services offered