Institution: ICVV
Research Groups: Structural Bioinformatics, Modeling and Biological Mechanisms
Position: Postdoc Researcher at Institute of Grapevine and Wine Sciences (ICVV)
Home page: https://model3dbio.csic.es/?page_id=246
Contact email: luisangel.rodriguez@icvv.es
BCB Committee: No committees assigned.
BCB Community: Bioinformatics tools, benchmarks and data visualization, Mathematical modeling in computational biology, Structural biology and molecular simulation
BCB Tools: pyDockDNA
BCB Services: No services assigned.
Research topics: Computational Methods, Applications of Computational Biology, Computational models and simulations, Biomolecular simulation, Biosystems Modeling, Structural bioinformatics, Molecular Interactions/Docking, Structure prediction, Structure-function relationship
Biography: I am Luis Ángel Rodríguez Lumbreras, PhD. I earned my Licentiate degree in Biochemistry from the University of Seville in 2013, a Master’s in Bioinformatics for Health Sciences from Pompeu Fabra University in 2015, and a PhD in Biomedicine, specializing in Bioinformatics, from the University of Barcelona in 2023.
I began my research career at the Department of Biochemistry and Molecular Biology at the University of Seville, where I studied the biochemical and biological properties of soil. I later joined the Barcelona Supercomputing Center (BSC) as a research student, focusing on protein modeling and the development of computational tools for predicting protein-protein and protein-DNA interactions. During this time, I contributed to the development of pyDockDNA.
Since 2019, I have been part of the Institute of Grapevine and Wine Sciences (ICVV), where I currently work as a postdoctoral researcher in the group led by Juan Fernández-Recio. My research focuses on structural bioinformatics and molecular modeling of protein complexes using artificial intelligence methods, with applications in both health and viticulture biotechnology.
I have participated in international initiatives such as CAPRI and CASP, and have published several articles in leading scientific journals. I am also the recipient of the BBVA-SEBBM Young Investigator Award and have contributed to the organization of scientific and educational events in bioinformatics.
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
Erausquin, E., Rodríguez-Fernández, A., Rodríguez-Lumbreras, L. Á., Fernández-Recio, J., Dichiara-Rodríguez, M. G., & López-Sagaseta, J. (2024). Structural vulnerability in EPCR suggests functional modulation. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-53160-7
Schweke, H., Xu, Q., Tauriello, G., Pantolini, L., Schwede, T., Cazals, F., Lhéritier, A., Fernandez‐Recio, J., Rodríguez‐Lumbreras, L. A., Schueler‐Furman, O., Varga, J. K., Jiménez‐García, B., Réau, M. F., Bonvin, A. M. J. J., Savojardo, C., Martelli, P., Casadio, R., Tubiana, J., Wolfson, H. J., … Wodak, S. J. (2023). Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study. PROTEOMICS, 23(17). Portico. https://doi.org/10.1002/pmic.202200323
Lensink, M. F., Brysbaert, G., Raouraoua, N., Bates, P. A., Giulini, M., Honorato, R. V., van Noort, C., Teixeira, J. M. C., Bonvin, A. M. J. J., Kong, R., Shi, H., Lu, X., Chang, S., Liu, J., Guo, Z., Chen, X., Morehead, A., Roy, R. S., Wu, T., … Wodak, S. J. (2023). Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 91(12), 1658–1683. Portico. https://doi.org/10.1002/prot.26609
Rodríguez-Lumbreras, L. A., Jiménez-García, B., Giménez-Santamarina, S., & Fernández-Recio, J. (2022). pyDockDNA: A new web server for energy-based protein-DNA docking and scoring. Frontiers in Molecular Biosciences, 9. https://doi.org/10.3389/fmolb.2022.988996
Castell, C., Rodríguez-Lumbreras, L. A., Hervás, M., Fernández-Recio, J., & Navarro, J. A. (2021). New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes. Plant and Cell Physiology, 62(7), 1082–1093. https://doi.org/10.1093/pcp/pcab044
Lensink, M. F., Brysbaert, G., Mauri, T., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Clarence, T., Bates, P. A., Kong, R., Liu, B., Yang, G., Liu, M., Shi, H., Lu, X., Chang, S., Roy, R. S., Quadir, F., Liu, J., Cheng, J., … Wodak, S. J. (2021). Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 89(12), 1800–1823. Portico. https://doi.org/10.1002/prot.26222
Varadi, M., Anyango, S., Armstrong, D., Berrisford, J., Choudhary, P., Deshpande, M., Nadzirin, N., Nair, S. S., Pravda, L., Tanweer, A., Al-Lazikani, B., Andreini, C., Barton, G. J., Bednar, D., Berka, K., Blundell, T., Brock, K. P., Carazo, J. M., … Velankar, S. (2021). PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Research, 50(D1), D534–D542. https://doi.org/10.1093/nar/gkab988
Rosell, M., Rodríguez-Lumbreras, L. A., & Fernández-Recio, J. (2020). Modeling of Protein Complexes and Molecular Assemblies with pyDock. Protein Structure Prediction, 175–198. https://doi.org/10.1007/978-1-0716-0708-4_10
Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., Kong, R., Liu, R., Xu, X., Shi, H., Chang, S., Eisenstein, M., Karczynska, A., Czaplewski, C., Lubecka, E., … Wodak, S. J. (2019). Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 87(12), 1200–1221. Portico. https://doi.org/10.1002/prot.25838
Rosell, M., Rodríguez‐Lumbreras, L. A., Romero‐Durana, M., Jiménez‐García, B., Díaz, L., & Fernández‐Recio, J. (2019). Integrative modeling of protein‐protein interactions with pyDock for the new docking challenges. Proteins: Structure, Function, and Bioinformatics, 88(8), 999–1008. Portico. https://doi.org/10.1002/prot.25858
Research lines:
There are no lines of investigation associated with this user.
Funding:
No funded projects.
More info
HPC Resources: Hidalgo, CESGA, BSC