Structural bioinformatics for wine sciences (3DBIOwine)

Group members: 
Juan Fernández Recio: 
CSIC Tenured Scientist
Luis Angel Rodríguez Lumbreras: 
CSIC Graduate Researcher
Mireia Rosell Oliveras: 
CSIC Graduate Researcher
Miguel Romero Durana: 
CSIC Postdoctoral Researcher
Structural bioinformatics for wine sciences (3DBIOwine)
Research Lines

The group has a clear multidisciplinary character, and its main research activity is the development and application of computational methods for the structural modeling of biomolecules of interest in grapevine and wine sciences.  The ultimate goal is to contribute to understand and rationally manipulate biomolecular processes related with wine, from the biosynthesis of metabolites in grapevine and further modification in vinification microorganisms, to their effects in human.

The specific aims are grouped in two major research lines, as detailed below:

  • 1. Development of computational tools for the structural and energetics modeling of biomolecular interactions. Our group has developed pioneering protein-protein docking methods, which are found among the most competitive ones at international level, according to objective evaluations, such as the CAPRI competition.
  • 1.1. One major goal is to continue developing new methods to try to overcome the limitations of current prediction methods: flexible proteins, weak interactions, multi-protein complexes, etc.
  • 1.2. Another goal is to extend these methods to the efficient prediction of other biomolecular interactions, such as protein-peptide, protein-nucleic acids, etc.
  • 2. Application to modeling of biomolecular interactions in organisms of interest for wine sciences: grapvine, microorganisms, and human. Specific aims within this line are:
  • 2.1. Interpretation of genetic variants in grapevine at the molecular level.
  • 2.2. Modeling and characterization of the molecular pathways of biosynthesis of metabolites of interest in grapevine and yeast.
  • 2.3. Understanding the molecular mechanisms of sensorial perception of wine.
  • 2.4. Molecular modeling to study the effects of relevant wine components in human health.
All publications(direct links)


Selected publications (last 5 years)

Errasti-Murugarren, E., Fort, J., Bartoccioni, P., Díaz, L., Pardon, E., Carpena, X., Espino-Guarch, M., Zorzano, A., Ziegler, C., Steyaert, J., Fernández-Recio, J., Fita, I., Palacin, M. (2019) L-amino acid transporter structure and molecular bases for the asymmetry of substrate interaction. Nat. Comm. 10, 1807.

Jankauskaité, J., Jiménez-García, B., Dapkūnas, J., Fernández-Recio, J., Moal, I.H. (2019) SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics 35, 462-469.

Rosell, M., Fernández-Recio, J. (2018) Hot-spot analysis for drug discovery targeting protein-protein interactions. Exp. Opin. Drug Discov. 13, 327-338.

Jiménez-García, B., Roel-Touris, J., Romero-Durana, M., Vidal, M., Jiménez-González, D., Fernández-Recio, J. (2018) LightDock: A new multi-scale approach to protein-protein docking. Bioinformatics 34, 49-55.

Barradas-Bautista, D., Fernández-Recio, J. (2017). Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations. PLoS One 12, e0183643.

Pallara, C., Jiménez-García, B., Romero-Durana, M., Moal, I.H., Fernández-Recio, J. (2017) pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions. Proteins 85, 487-496.

Pallara, C., Rueda, M., Abagyan, R., Fernández-Recio, J. (2016) Conformational heterogeneity of unbound proteins enhances recognition in protein-protein encounters. JCTC 12, 3236-3249.

Jiménez-García, B., Pons, C., Svergun, D.I., Bernadó, P., Fernández-Recio, J. (2015) pyDockSAXS: protein-protein complex structure by SAXS and computational docking. Nucleic Acids Res. 43, W356-361.

Moal, I.H., Jiménez-García, B., Fernández-Recio, J. (2015) CCharPPI web server: Computational Characterisation of Protein-Protein Interactions from structure. Bioinformatics 31, 123-125.

Lucas, M., Gaspar, A.H., Pallara, C., Rojas, A.L., Fernández-Recio, J., Machner, M.P., Hierro, A. (2014) Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5. Proc Natl Acad Sci USA 111, E3514-E3523.

Rosell, A., Meury, M., Alvarez-Marimon, E., Costa, M., Pérez-Cano, L., Zorzano, A., Fernández-Recio, J., Palacín, M., Fotiadis, D. (2014) Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc. Proc Natl Acad Sci USA 111, 2966-2971.