Research group

Applications of Computational Biology, Biomolecular simulation, Biosystems Modeling, Computational Methods, Computational models and simulations, Drug Discovery and design, Molecular Interactions/Docking, Structural bioinformatics, Structure prediction, Structure-function relationship

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 <scp>AlphaFold</scp> on structure prediction of protein complexes: The <scp>CASP15‐CAPRI</scp> 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 <scp>CASP14‐CAPRI</scp> 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