Research Outline

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. We 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.

Current Projects

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.

On 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.

On 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.

Selected publications 2012-2015


  • Wright RH, Castellano G, Bonet J, Le Dily F, Font-Mateu J, Ballaré C, Nacht AS, Soronellas D, Oliva B, Beato M. CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells. Genes Dev, 2012; 26(17):1972-83
  • Garcia-Garcia J, Schleker S, Klein-Seetharaman J, Oliva B. BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference Nucleic Acids Res, 2012; 40 (W1):W147-W151
  • Guney E, Oliva B. Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization. PLoS One, 2012, 7 (9) e43557
  • Santana-Codina N, Carretero R, Sanz-Pamplona R, Cabrera T, Guney E, Oliva B, Clezardin P, Olarte OE, Loza-Alvarez P, Méndez-Lucas A, Perales JC, Sierra A. A transcriptome-proteome integrated network identifies ERp57 as a hub that mediates bone metastasis. Mol Cell Proteomics, 2013; 12(8): 2111-2125
  • Planas-Iglesias J, Bonet J, García-García J, Marín-López MA, Feliu E, Oliva B. Understanding protein-protein interactions using local structural features. J Mol Biol, 2013; 425 (7):1210-1224
  • Bonet, J, Planas-Iglesias, J, Garcia-Garcia, J, Marin-Lopez,MA, Fernandez-Fuentes, N., Oliva, B. ArchDB 2014: structural classification of loops in proteins. Nucleic Acids Research, 2014; 42(Database issue):D315-9
  • Guney, E., Garcia-Garcia,J, Oliva, B. GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. Bioinformatics 2014;30(12):1789-90
  • Oliva,B. & Fernandez-Fuentes, N. Knowledge-based modeling of peptides at protein interfaces: PiPreD. Bioinformatics. 2015; 31(9): 1405-10



For more information about completed and ongoing projects please check:

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