Structural Bioinformatics, Modeling and Biological Mechanisms

Institution: Instituto de Ciencias de la Vid y del Vino (ICVV)

Members (researchers): Luis Ángel Rodríguez Lumbreras, Víctor Monteagudo Honrubia, Juan Fernández Recio

Home page: https://model3dbio.csic.es/
Contact email: juan.fernandezrecio@icvv.es

Tools: pyDockDNA, pyDock

Service Units: Cellular, Molecular and Bioinformatics Service at ICVV

The group is focused to the theoretical study of biological phenomena at molecular level and the development of computer tools for the analysis, structural prediction and characterization of protein interactions, with key contributions in the field, like the ASA-based desolvation description, later implemented in other docking methods, or the pyDock docking and scoring program. The group consistently ranks highly in the CASP and CAPRI international blind assessment experiments, which shows the competitive capabilities of the computer tools developed in the group. The group is actively involved in many multi-disciplinary collaborative projects for the study of protein interactions of biomedical and biotechnological interest, with applications to practical challenges such as the interpretation of genetic variants and the identification of small-molecule modulators of protein interactions.

Research topics:

Analysis packages (R, Python, etc.), Applications of Computational Biology, Artificial Intelligence, Bayesian statistics, Bioinformatics Software and Tools, Biomolecular simulation, Biosystems Modeling, Computational Methods, Computational models and simulations, Data Analysis, Drug Discovery and design, Machine Learning in Biology, Molecular flexibility, Molecular Interactions/Docking, Multivariate statistics, Mutation Analysis and design, Population dynamics, Protein/Nucleic Acid design, Proteing-Protein Interactions, Proteomics, Statistical Methods for Biology, Structural bioinformatics, Structural genomics, Structure prediction, Structure-function relationship


Publications

Jiménez-Panizo, A., Johnson, T. A., Wagh, K., Alegre-Martí, A., Novoa, I. M., Lafuente, A. L., Eckhard, U., Rodríguez-Lumbreras, L. Á., Hoang, L., Stortz, M., Abella, M., Goldstein, I., Valledor-Fernández, A., Varticovski, L., Arias, I., Presman, D. M., Stavreva, D. A., Fernández-Recio, J., Fuentes-Prior, P., … Estébanez-Perpiñá, E. (2025). Bile acids target an exposed cavity in the glucocorticoid receptor modulating receptor self-assembly, chromatin binding and transcriptional activity. https://doi.org/10.1101/2025.05.13.653693

Venezian, J., Bar-Yosef, H., Ben-Arie Zilberman, H., Cohen, N., Kleifeld, O., Fernandez-Recio, J., Glaser, F., & Shiber, A. (2024). Diverging co-translational protein complex assembly pathways are governed by interface energy distribution. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-46881-w