Lab Presentation

Our group works on theoretical and computational approaches to study protein-protein association at structural and energetic level. We are developing new computational methods for modeling protein-protein complex structure by docking, prediction of binding sites and hot-spot residues, and understanding the specificity of protein-nucleic acid interactions. On the most practical side, we are modeling protein interactions of biological and therapeutic interest, related to signal transduction, amino acid transport or gene regulation. The ultimate goal of our research is to apply our models to the interpretation of pathological mutations involved in protein interactions, and to drug discovery.

 

 

The main goal of the group is to contribute to solve some of the important challenges in the structural biology of protein-protein and protein-nucleic acid interactions. These are our major research lines:

Development of new computational tools for protein-protein docking and binding site prediction. We are developing tools for more efficient identification of correct docking poses, especially in difficult cases such as weak interactions, multi-protein complexes or membrane proteins. One important aspect is the inclusion of conformational flexibility by using conformational ensembles precomputed from the unbound proteins, interface refinement, coarse-grained stochastic models for flexible docking, and the integration of low-resolution structural data from SAXS.

Structural bioinformatics for the characterization and modeling of protein-nucleic acid interactions. We are developing new methods for protein-RNA and protein-DNA binding. This will have applications in the multi-scale modeling of macro-complexes, such as transcriptional complexes, nucleosome or chromatin.

Understanding binding affinity, kinetics and mechanism of macromolecular association. We are working on new theoretical models of protein association mechanism by analysis of docking energy landscapes, and more accurate description of the binding energy.

Structural modeling of cases of biomedical interest and drug discovery. We are applying our models to study cases of biomedical interest, in collaboration with experimental laboratories, related to transmembrane signalling, heteromeric amino acid transporting, or gene regulation. We also aim to contribute to drug discovery targeting protein-protein interactions by means of identification of transient cavities based on molecular dynamics, docking-based hot-spot prediction, and integration of protein-protein and protein-ligand computational simulations.

Molecular interpretation of pathological mutations involved in protein interactions. We are applying our docking methods to study rare diseases included in newborn screening programs, in order to understand better the effect of sequence variants in pathological conditions when they are involved in protein-protein interactions for which there is no structural data available. Our protein interaction predictions can help to annotate and interpret sequence variation data for personalized medicine.

Projects

  • Methodology development for protein-protein docking. Read more
  • Understanding binding affinity and specificity of macromolecular interactions: protein-protein, and protein-nucleic acids. Read more
  • Modeling protein interactions of biomedical interest and drug discovery. Read more
  • Interpretation of pathological mutations involved in protein-protein interactions for precision diagnosis and therapeutics. Read more
  • Previously developed web servers, databases and tools. Read more

Lab People

Juan Fernández Recio

Juan Fernández Recio

Tenured Scientist CSIC

jfrcri@ibmb.csic.es

Dr. Fernández-Recio is leading the Protein Interactions and Docking group, at the Institut de Biologia Molecular de Barcelona (IBMB). In 1994, he graduated in Chemistry (Organic Chemistry specialty) from the University of Zaragoza, and in 1999, he received his PhD in Chemistry (Biochemistry and Molecular and Cell Biology program) from the same university, under the supervision of Profs. Carlos Gómez-Moreno and Javier Sancho. During 1999-2003, he worked on theoretical approaches to the study of protein interactions as a Research Associate in the laboratory of Prof. Ruben Abagyan, at The Scripps Research Institute (TSRI), La Jolla CA, US. Then he worked as a Marie Curie Research Fellow (2003-2004) in the computational and crystallography laboratory of Prof. Sir Tom Blundell, at the University of Cambridge (UK). At the end of 2004, he set up his own group at the Parc Scientific de Barcelona (PCB), as a Ramón y Cajal researcher, and in 2007, he got a position as Research Group Leader at the Barcelona Supercomputing Center (BSC). In 2017, he joined IBMB (CSIC) as a Tenured Scientist.

Lucía Díaz Bueno

Lucía Díaz Bueno

Postdoctoral Researcher

lucia.diaz@bsc.es

Brian Jiménez García

Brian Jiménez García

Postdoctoral Researcher

bjimenez@bsc.es

Miguel Romero

Miguel Romero

PhD student

miguel.romero@bsc.es

Mireia Rosell

Mireia Rosell

PhD student

mireia.rosell@bsc.es

Luis Ángel Rodríguez Lumbreras

Luis Ángel Rodríguez Lumbreras

PhD student

luis.rodriguez@bsc.es

Silvia Giménez Santamarina

Silvia Giménez Santamarina

PhD student
Bruno Cuevas Zuviria

Bruno Cuevas Zuviria

Visiting Graduate Student
Dàmaris Navío Maya

Dàmaris Navío Maya

Master Student
César González Griñán

César González Griñán

Master Student

cesar.gonzalez@bsc.es

Selected Publications


LightDock: A new multi-scale approach to protein-protein docking.

B. Jiménez-García, J. Roel-Touris, M. Romero-Durana, M. Vidal, D. Jiménez-González, J. Fernández-Recio

Bioinformatics (in press) (2017)


Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations.

D. Barradas-Bautista, J. Fernández-Recio

PLoS One 12, e0183643. (2017)


Conformational heterogeneity of unbound proteins enhances recognition in protein-protein encounters.

C. Pallara, M. Rueda, R. Abagyan, J. Fernández-Recio

JCTC 12, 3236-3249 (2016)


pyDockSAXS: protein-protein complex structure by SAXS and computational docking.

B. Jiménez-García, C. Pons, D.I. Svergun, P. Bernadó, J. Fernández-Recio

Nucleic Acids Res. 43:W356-361. (2015)


CCharPPI web server: Computational Characterisation of Protein-Protein Interactions from structure.

Moal, I.H., Jiménez-García, B., J. Fernández-Recio

Bioinformatics 31, 123-125. (2015)


Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc.

A. Rosell, M. Meury, E. Alvarez-Marimon, M. Costa, L. Pérez-Cano, A. Zorzano, J. Fernández-Recio*, M. Palacín*, D. Fotiadis*  * Corresponding authors

Proc Natl Acad Sci USA. 111, 2966-2971.  (2014)


Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.

M. Lucas, A.H, Gaspar, C. Pallara, C., A.L. Rojas, J. Fernández-Recio, M.P.Machner, A.Hierro.

Proc Natl Acad Sci USA 111, E3514-E3523. (2014)


Conformational transitions in human translin enable nucleic acid binding.

L. Pérez-Cano, E. Eliahoo, K. Lasker, H.J. Wolfson, F. Glaser, H. Manor, P. Bernadó, J. Fernández-Recio

Nucleic Acids Res. 41, 9956-9966. (2013)


SKEMPI: A Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.

I.H. Moal, J. Fernández-Recio

Bioinformatics 28, 2600-2607.EMBO J. (2012)


Prediction of protein binding sites and hot spots.

J. Fernández-Recio

WIREs Comput. Mol. Sci. 1, 680-698 (2011)


Present and future challenges and limitations in protein-protein docking.

C. Pons, S. Grosdidier, A. Solernou, L. Pérez-Cano,  J. Fernández-Recio (2010)

Proteins 78, 95-108. (2010)


pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.

T. Cheng, T.L. Blundell, J. Fernández-Recio

Proteins 68, 503-515. (2007)


All Publications


LightDock: A new multi-scale approach to protein-protein docking.

Jiménez-García, B., Roel-Touris, J., Romero-Durana, M., Vidal, M., Jiménez-González, D., Fernández-Recio, J.

Bioinformatics (in press) (2017)


Structural prediction of protein-protein interactions by docking: application to biomedical problems.

Barradas-Bautista, D., Rosell, M., Pallara, C., Fernández-Recio, J.

 Adv. Prot. Chem. Struct. Biol. (in press) (2017)


Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations.

Barradas-Bautista, D., Fernández-Recio, J.

PLoS One 12, e0183643. (2017)


A systematic analysis of scoring functions in rigid-body protein docking: the delicate balance between the predictive rate improvement and the risk of overtraining.

Barradas-Bautista, D., Moal, I.H., Fernández-Recio, J.

Proteins 85, 1287-1297. (2017)


RaPPA: Information retrieval based integration of biophysical models for protein assembly selection.

Moal, I.H., Barradas-Bautista, D., Jiménez-García, B, Torchala, M., van der Veide, A, Vreven, T., Weng, Z., Bates, P.A., Fernández-Recio, J. (2017) I

Bioinformatics 33, 1806-1813 (2017)


Modeling binding affinity of pathological mutations for computational protein design.

Romero-Durana, M., Pallara, C., Glaser, F., Fernández-Recio, J.

Methods Mol.Biol. 1529, 139-159. (2017)


pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions.

Pallara, C., Jiménez-García, B., Romero-Durana, M., Moal, I.H., Fernández-Recio, J.

Proteins 85, 487-496. (2017)


Structural and energy determinants in protein-RNA docking.

Pérez-Cano, L., Romero-Durana, M., Fernández-Recio, J.

Methods 118-119, 163-170. (2017)


Optimization of protein-protein docking for predicting Fc-protein interactions.

Agostino, M., Mancera, R.L., Ramsland, P.A., Fernández-Recio, J.

J.Mol. Recognit. 29, 555-568. (2016)


Structural prediction of receptor binding to IgM and IgA. 

Agostino, M., Mancera, R.L., Fernández-Recio, J., Ramsland, P.A.

Eur. J. Immunol. 46 (Suppl 1), 476-476. (2016)


Unraveling the molecular details of the innate immune response.

Fernández-Recio, J.

EBioMedicine 9, 7-8. (2016)


Conformational heterogeneity of unbound proteins enhances recognition in protein-protein encounters.

Pallara, C., Rueda, M., Abagyan, R., Fernández-Recio, J.

JCTC 12, 3236-3249. (2016)


Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.

Lensink M.F et al. (total 102 authors, including Fernández-Recio, J.)

Proteins 84 (Suppl 1), 323-348. (2016)


Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor.

Bernal-Bayard, P., Pallara, C., Castell, M.C., Molina-Heredia, F.P., Fernández-Recio, J., Hervás, M., Navarro, J.A.

IBBA-Bioenergetics 1847, 1549-1559. (2015)


Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

Vreven, T., Moal, I.H., Vangone, A., Pierce, B.G., Kastritis, P.L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P.A., Fernandez-Recio, J., Bonvin, A.M., Weng, Z.

J.Mol.Biol. 427, 3031-3041. (2015)


pyDockSAXS: protein-protein complex structure by SAXS and computational docking.

Jiménez-García, B., Pons, C., Svergun, D.I., Bernadó, P., Fernández-Recio, J.

Nucleic Acids Res. 43:W356-361. (2015)


EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGF.

Khayati, F., Pérez-Cano, L., Maouche, K., Sadoux, A., Boutalbi, Z., Podgorniak, M-P., Maskos, U., Setterblad, N., Janin, A., Calvo, F., Lebbe, C., Menashi, S., Fernández-Recio, J., Mourah, S.

Oncotarget 6, 9766-9780. (2015)


Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction.

Somajo S., Ahnström, J., Fernandez-Recio, J., Gierula, M., Villoutreix, B.O., Dahlbäck, B.

Thromb Haemost. 113, 976-987. (2015)


Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

Moal, I.H., Dapkunas, J., Fernández-Recio, J.

Proteins 83, 640-650. (2015)


Comment on ‘protein-protein binding affinity prediction from amino acid sequence’.

Moal, I.H., Fernández-Recio, J.

Bioinformatics 31, 614-615. (2015)


CCharPPI web server: Computational Characterisation of Protein-Protein Interactions from structure.

Moal, I.H., Jiménez-García, B., Fernández-Recio, J.

Bioinformatics 31, 123-125. (2015)


EMMPRIN/CD147 is a co-receptor for VEGFR-2 in tumor angiogenesis: towards its inhibition.

Khayati, F., Fernández-Recio, J., Pérez, L., Villoutreix, B., Calvo, F., Lebbe, C., Menashi, S., Mourah, S.

Fund. Clin. Pharm. 28, 4-4. (2014)


Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.

Lucas, M., Gaspar, A.H., Pallara, C., Rojas, A.L., Fernández-Recio, J., Machner, M.P., Hierro, A.

Proc Natl Acad Sci USA 111, E3514-E3523. (2014)


Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity.

Lang, V., Pallara, C., Zabala, A., Lobato-Gil, S., Lopitz-Otsoa, F., Farrás, R., Hjerpe, R., Torres-Ramos, M., Zabaleta, L., Blattner, C., Hay, R.T., Barrio, R., Carracedo, A., Fernandez-Recio, J., Rodríguez, M.S., Aillet, F.

Mol. Oncol. 8, 1026-1042. (2014)


Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc.

Rosell, A., Meury, M., Alvarez-Marimon, E., Costa, M., Pérez-Cano, L., Zorzano, A., Fernández-Recio, J.*, Palacín, M.*, Fotiadis, D.* *Corresponding authors

Proc Natl Acad Sci USA 111, 2966-2971. (2014)


Blind prediction of interfacial water positions in CAPRI.

Lensink, M.F. et al. (total 58 authors, including Fernández-Recio, J.)

Proteins 82, 620-632. (2014)


Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation.

Moal, I.H., Fernandez-Recio, J.

J. Chem. Theory Comput. 9, 3715-3727. (2013)


The scoring of poses in protein-protein docking: current capabilities and future directions.

Moal, I.H., Torchala, M., Bates, P.A., Fernandez-Recio, J. (2013)

BMC Bioinformatics 14, 286. (2013)


Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.

Agius, R., Torchala, M., Moal, I.H., Fernandez-Recio, J., Bates, P.A.

PLoS Comput. Biol. 9, e1003216. (2013)


Conformational transitions in human translin enable nucleic acid binding.

Pérez-Cano, L., Eliahoo, E., Lasker, K., Wolfson, H.J., Glaser, F., Manor, H., Bernadó, P., Fernández-Recio, J.

Nucleic Acids Res. 41, 9956-9966. (2013)


Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges.

Pallara, C., Jiménez-García, B., Pérez-Cano, L., Romero-Durana, M., Solernou, A., Grosdidier, S., Pons, C., Moal, I.H., Fernández-Recio, J.

Proteins 81, 2192-2200. (2013)


Scoring functions for protein-protein interactions.

Moal, I.H., Moretti, R., Baker, D., Fernandez-Recio, J.

Curr. Opin. Struct. Biol. 23, 862-867. (2013)


Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Moretti, R. et al. (total 70 authors, including Fernández-Recio, J.) (2013)

Proteins 81, 1980-1987. (2013)


Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD.

Chen, Y., Tascón, I., Neunuebel, M.R., Pallara, C., Brady, J., Kinch, L.N., Fernández-Recio, J., Adriana L. Rojas, A.L., Machner, M.P., Hierro, A.

PLOS Pathogens 9, e1003382. (2013)


pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

Jiménez-García, B., Pons, C., Fernandez-Recio, J.

Bioinformatics 29, 1698-1699. (2013)


Validated conformational ensembles are key for the successful prediction of protein complexes.

Pons, C., Fenwick, R.B., Esteban-Martín, S., Salvatella, X., Fernandez-Recio, J.

J. Chem. Theory Comput. 9, 1830-1837. (2013)


Efficient Relaxation of Protein–Protein Interfaces by Discrete Molecular Dynamics Simulations.

Emperador, A., Solernou, A., Sfriso, P., Pons, C., Gelpi, J.L., Fernandez-Recio, J.*, Orozco, M.* *Corresponding authors

J. Chem. Theory Comput. 9, 1222-1229. (2013)


SwarmDock: a server for flexible protein-protein docking.

Torchala, M., Moal, I.H., Chaleil, R.A., Fernandez-Recio, J., Bates, P.A.

Bioinformatics 29, 807-809. (2013)


SKEMPI: A Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.

Moal, I.H., Fernandez-Recio, J.

Bioinformatics 28, 2600-2607. (2012)


Cell-Dock: high-performance protein-protein docking.

Pons C, Jiménez-González D, González-Álvarez C, Servat H, Cabrera-Benítez D, Aguilar X, Fernández-Recio J. (2012)

Bioinformatics 28, 2394-2396. (2012)


Protein-protein docking and hot-spot prediction for drug discovery.

Grosdidier, S., Fernández-Recio, J.

Curr Pharm Des. 18, 4607-4618. (2012)


Allosteric Conversation in the Androgen Receptor Ligand-Binding Domain Surfaces.

Grosdidier, S., Carbó, L.R., Buzón, V., Brooke, G., Nguyen, P., Baxter, J.D., Bevan, C., Webb, P., Estébanez-Perpiñá, E., Fernández-Recio, J.

Mol. Endocrinol. 26, 1078-1090. (2012)


A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data.

Pérez-Cano, L., Jiménez-García, B., Fernández-Recio, J.

Proteins 80, 1872-1882. (2012)


Theory and simulation: complexity and emergence.

Fernández-Recio, J., Verma, C.

Curr Opin Struct Biol. 22, 127-129. (2012)


H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?

Masone, D., Vaca, I.C., Pons, C., Fernández-Recio, J., Guallar, V.

Proteins 80, 818-824. (2012)


Established and emerging trends in computational drug discovery in the structural genomics era.

Taboureau, O., Baell, J.B., Fernández-Recio, J., Villoutreix, B.O.

Chem Biol. 19, 29-41. (2012)


Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Fleishman, S. et al. (total 96 authors, including Fernández-Recio, J.)

J. Mol. Biol. 414, 289-302. (2011)


Prediction of protein-binding areas by small-world residue networks and application to docking.

Pons, C., Glaser, F., Fernández-Recio, J.

BMC Bioinformatics 12:378. (2011)


LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.

Helft, L., Reddy, V., Chen, X., Koller, T., Federici, L., Fernández-Recio, J., Gupta, R., Bent, A.

PLoS One 6, e21614. (2011)


Prediction of protein binding sites and hot spots.

Fernández-Recio, J.

WIREs Comput. Mol. Sci. 1, 680-698. (2011)


pyDockCG: new coarse-grained potential for protein-protein docking. 

Solernou, A., Fernández-Recio, J.

J. Phys. Chem. B 115, 6032-6039. (2011)


Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A new efficient potential for protein-protein docking.

Pons, C., Talavera, D., de la Cruz, X., Orozco, M., Fernández-Recio, J.

J. Chem. Inf. Mod. 51, 370-377. (2011)


Dissection and prediction of RNA-binding sites on proteins.

Pérez-Cano, L., Fernández-Recio, J.

BioMol Concepts 1, 345-355. (2010)


Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.

Pons, C., D’Abramo, M., Svergun, D., Orozco, M., Bernadó, P., Fernández-Recio, J.

J. Mol. Biol. 403, 217-230. (2010)


The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona.

Fernández-Recio, J., Sternberg, M.

Proteins 78, 3065-3066. (2010)


Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.

Pons, C., Solernou, A., Pérez-Cano, L., Grosdidier, S., Fernández-Recio, J.

Proteins 78, 3182-3188. (2010)


Interdomain conformations in the full-length MMP-2 enzyme explored by protein-protein docking calculations using pyDock.

Valdes, H., Diaz, N., Suarez, D., Fernández-Recio, J.

J. Chem. Theory Comput. 6, 2204-2213. (2010)


Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation.

Solernou, A., Fernández-Recio, J.

BMC Bioinformatics 11, 352. (2010)


Theory and simulation: integrating models into experimental scenarios.

Fernández-Recio, J., Verma, C.

Curr. Opin. Struct. Biol. 20, 139-141. (2010)


Refinement of rigid-body protein-protein docking using backbone and side-chain minimization with a coarse-grained model.

Solernou, A., Fernández-Recio, J.

Open Access Bioinformatics 2, 19-27. (2010)


Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study.

Eliahoo, E., Ben Yosef, R., Pérez-Cano, L., Fernández-Recio, J., Glaser, F., Manor, H.

Nucleic Acids Res. 38, 2975-2989. (2010)


Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine.

Alías, M., Ayuso-Tejedor, S., Fernández-Recio, J., Cativiela, C., Sancho, J.

POrg. Biomol. Chem. 8, 788-792. (2010)


Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials.

Pérez-Cano, L., Fernández-Recio, J.

Pac. Symp. Biocomput. 2010, 293-301. (2010)


Present and future challenges and limitations in protein-protein docking.

Pons, C., Grosdidier, S., Solernou A., Pérez-Cano, L., Fernández-Recio, J.

Proteins 78, 95-108. (2010)


Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins.

Pérez-Cano, L., Fernández-Recio, J.

Proteins 78, 25-35. (2010)


On the use of low-resolution data to improve structure prediction of proteins and protein complexes.

D’Abramo, M., Meyer, T., Bernadó, P., Pons, C., Fernández-Recio, J., Orozco, M.

J. Chem. Theory Comput. 5, 3129-3137. (2009)


Computer applications for prediction of protein-protein interactions and rational drug design.

Grosdidier, S., Totrov, M., Fernández-Recio, J.

Adv. Appl. Bioinf. Chem. 2, 1-23. (2009)


Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

Mosca, R., Pons, C., Fernández-Recio, J. Aloy P.

PLoS Comput Biol. 5, e1000490. (2009)


FRODOCK: a new approach for fast rotational protein-protein docking.

Garzon, J.I., Lopéz-Blanco, J.R., Pons, C., Kovacs, J., Abagyan, R., Fernández-Recio, J., Chacon, P.

Bioinformatics 25, 2544-2551. (2009)


Docking and scoring: applications to drug discovery in the proteomics era.

Grosdidier, S., Fernández-Recio, J.

Expert Opin. Drug Discov. 4, 673-686. (2009)


Predicting protein-protein interfaces as clusters of optimal docking area points.

Arafat, Y., Kamruzzaman, J., Karmakar, G.C., Fernández-Recio, J.

Int. J. Data Mining Bioinf. 3, 55-67. (2009)


Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein.

Casasoli, M., Federici, L., Spinelli, F., Di Matteo, A., Vella, N., Scaloni, F., Fernández-Recio, J., Cervone, F., De Lorenzo, G.

Proc. Natl. Acad. Sci. USA. 106, 7666-7671. (2009)


Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering.

Bernadó, P., Pérez, Y., Blobel, J., Fernández-Recio, J., Svergun, D.I., Pons, M.

Protein Sci. 18, 716-726. (2009)


Computational tools for exploration of the energy landscape in protein-protein association.

Solernou, A., Fernández-Recio, J.

AIP Conf. Proc. 1071, 98-108. (2008)


Identification of hot-spot residues in protein-protein interaction by computational docking.

Grosdidier, S., Fernández-Recio, J.

BMC Bioinformatics 9, 447. (2008)


Structural assembly of two-domain proteins by rigid-body docking.

Cheng, T.M.K.., Blundell, T.L., Fernández-Recio, J.

BMC Bioinformatics 9, 441. (2008)


Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum.

Hart, S.E., Howe, C.J., Mizuguchi, K., Fernández-Recio, J.

Protein Eng. Des. Sel. 21, 689-698. (2008)


Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid).

Pallarès, I., Fernández, D., Comellas-Bigler, M., Fernández-Recio, J., Ventura, S., Avilés, F.X., Bode, W., Vendrell, J.

Acta Crystallogr. D Biol.Crystallogr. 64, 784-791. (2008)


In silico docking of urokinase plasminogen activator and integrins.

Degryse, B., Fernandez-Recio, J., Citro, V., Blasi, F., Cubellis, M.V.

BMC Bioinformatics 9 (Suppl 2), S8. (2008)


Theory and simulation. Editorial overview.

Fernández-Recio, J., Verma, C.

ICurr.Opin.Struct.Biol. 18, 131-133. (2008)


Assembly and channel opening in a bacterial drug efflux machine.

Bavro, V., Pietras, Z., Furnham, N., Pérez-Cano, L., Fernández-Recio, J., Yuan Pei, X., Misra, R., Luisi, B.

Mol. Cell. 30, 114-121. (2008)


Docking analysis of transient complexes: Interaction of ferredoxin.NADP+ reductase with ferredoxin and flavodoxin.

Medina, M., Abagyan, R,, Gómez-Moreno, C., Fernández-Recio, J.

Proteins 72, 848-862. (2008)


Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.

Bonivento, D., Pontiggia, D., Di Matteo, A., Fernández-Recio, J., Salvi, G., Tsernoglou, D., Cervone, F., De Lorenzo, G., Federici, L.

Proteins 70, 294-299. (2008)


Prediction and scoring of docking poses with pyDock.

Grosdidier, S., Pons, C., Solernou, A., Fernandez-Recio, J.

Proteins 69, 852-858. (2007)


The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.

Fort, J., de la Ballina, L.R., Burghardt, H.E., Ferrer-Costa, C., Turnay, J., Ferrer-Orta, C., Usón, I., Zorzano, A., Fernández-Recio, J., Orozco, M., Lizarbe, M.A., Fita, I., Palacín, M.

J.Biol.Chem. 282, 31444-31452. (20017


pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.

Cheng, T., Blundell, T.L., Fernández-Recio, J.

Proteins 68, 503-515. (2007)


Structural and functional characterization of binding sites in metallopeptidases based on ODA analysis.

Fernández, D., Vendrell, J., Avilés, F.X., Fernández-Recio, J.

Proteins. 68, 131-144. (2007)


Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.

Chandran, V., Poljak, L., Vanzo, N.F., Leroy, A., Miguel, R.N., Fernandez-Recio, J., Parkinson, J., Burns, C., Carpousis, A.J., Luisi, B.F.

J.Mol.Biol. 367, 113-132. (2007)


Brief encounters bolster contacts.

Blundell, T.L., Fernández-Recio, J.

Nature 444, 279-280. (2006)


Identifying interaction motifs in CK2beta – a ubiquitous kinase regulatory subunit?

Bolanos-Garcia, V., Fernández-Recio, J., Allende, J.E., Blundell, T.L.

Trends Biochem. Sci. 31, 654-661. (2006)


The crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition.

Casal, E., Federici, L., Zhang, W., Fernández-Recio, J., Priego, E.M., Núñez-Miguel, R., DuHadaway, J.B., Prendergast, G.C., Luisi, B.F., Laue, E.

Biochemistry 45, 12917-12928. (2006)


New Efficient Substrates for Semicarbazide-Sensitive Amine Oxidase/VAP-1 Enzyme: Analysis by SARs and Computational Docking.

Yraola, F., García-Vicente, S., Fernández-Recio, J., Albericio, F., Zorzano, A., Marti, L., Royo, M.

J.Med.Chem. 49, 6197-6208. (2006)


Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching.

Arafat, Y., Karmakar, G., Kamruzzaman, J., Fernández-Recio, J.

In CIBCB 2006 IEEE Symp. p. 1-8. ISBN 1-4244-0624-2. (2006)


Data mining of molecular dynamics trajectories of nucleic acids.

Noy, A., Meyer, T., Rueda, M., Ferrer, C., Valencia, A., Perez, A., de la Cruz, X., Lopez-Bes, J.M., Pouplana, R., Fernández-Recio, J., Luque, F.J., Orozco, M.

J Biomol Struct Dyn. 23, 447-456. (2006)


Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. 

Chelliah, V., Blundell, T.L., Fernández-Recio, J.

J.Mol.Biol. 357, 1669-1682.  (2006)


Polygalacturonase inhibiting proteins: players in plant innate immunity?

Federici, L., Di Matteo, A., Fernández-Recio, J., Cervone, F., Tsernoglou, D.

Trends in Plant Science. 11, 65-70. (2006)


The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endo-polygalacturonase PG1 of Botrytis cinerea.

Sicilia, F., Fernández-Recio, J., Caprari, C., De Lorenzo, G., Tsernoglou, D., Cervone, F., Federici, L.

Plant Physiology 139, 1380-1388. (2005)


Improving CAPRI predictions: optimized desolvation for rigid-body docking.

Fernández-Recio, J., Abagyan, R., Totrov, M.

Proteins 60, 308-313. (2005)


The crystal structure of the outer membrane protein VceC form the bacterial pathogen Vibrio cholerae at 1.8 Å resolution.

Federici, L., Du, D., Walas, F., Matsumura, H., Fernández-Recio, J., Borges-Walmsley, I., Luisi, B.F., Walmsley, A.

J.Biol.Chem. 280, 15307-15314. (2005)


Optimal Docking Area: a new method for predicting protein-protein interaction sites.

Fernández-Recio, J., Totrov, M., Skorodumov, C., Abagyan, R.

Proteins 58, 134-143. (2005)


A model of a transmembrane drug-efflux pump from Gram-negative bacteria.

Fernández-Recio, J., Walas, F., Federici, L., Pratap J.V., Bavro, V., Miguel R.N., Mizuguchi K., Luisi, B.

FEBS Lett. 578, 5-9. (2004)


The long and short flavodoxins. II: role of the differentiating loop in apoflavodoxin stability and folding mechanism.

López-Llano, J., Maldonado, S., Jain, S., Lostao, A., Godoy-Ruiz, R., Sanchez-Ruiz, J.M., Cortijo, M., Fernández-Recio, J. , Sancho J.

J.Biol.Chem. 279, 47184-47191. (2004)


The crystal structure of Fibroblast Growth Factor (FGF) 19 reveals novel features of the FGF family and offers a structural basis for its unusual receptor affinity.

Harmer, N.J., Pellegrini, L., Chirgadze, D., Fernández-Recio, J., Blundell, T.L.

Biochemistry 43, 629-640. (2004)


Identification of Protein-Protein Interaction Sites from Docking Energy Landscapes.

Fernández-Recio, J., Totrov, M., Abagyan, R.

J.Mol.Biol. 335, 843-865. (2004)


ICM-DISCO Docking by Global Energy Optimization with Fully Flexible Side-Chains.

Fernández-Recio, J., Totrov, M., Abagyan, R.

Proteins 52, 113-117. (2003)


The ‘relevant’ stability of proteins with equilibrium intermediates.

Sancho, J., Bueno, M., Campos, L.A., Fernández-Recio, J., Irún, M.P., Machicado, C., Pedroso, I., Toja, M.

The Scientific World Journal 2, 1209-1215. (2002)


Soft protein-protein docking in internal coordinates.

Fernández-Recio, J., Totrov, M., Abagyan, R.

Protein Sci. 11, 280-291. (2002)


Screened charge electrostatic model in protein-protein docking simulations.

Fernández-Recio, J., Totrov, M., Abagyan, R.

Pac. Symp. Biocomput. 7, 552-563. (2002)


Apoflavodoxin folding mechanism: an a/b protein with an essentially off-pathway intermediate. 

Fernández-Recio, J., Genzor, C.G., Sancho, J.

Biochemistry 40, 15234-15245.  (2001)


Modulation of electroenzymatic NADPH oxidation through oriented immobilization of ferredoxin:NADP+ reductase onto modified gold electrodes.

Madoz-Gúrpide, J., Abad, J.M., Fernández-Recio, J., Vélez, M., Vázquez, L., Gómez-Moreno, C., Fernández, V.M.

J. Am. Chem. Soc. 122, 9808-9817 (2000)


Sensitive potential for protein-protein docking.

Abagyan, R., Totrov, M., Fernández-Recio, J.

Abstr. Pap. Am. Chem. Soc. 218, 205. (1999)


Energetics of a hydrogen bond (charged and neutral) and of a cation-p interaction in apoflavodoxin.

Fernández-Recio, J., Romero, A., Sancho, J.

J. Mol. Biol. 290, 319-330. (1999)


Investigation of the diaphorase reaction of ferredoxin-NADP+ reductase by electrochemical methods. 

Madoz, J., Fernández-Recio, J., Gómez-Moreno, C., Fernández, V.M.

Bioelectrochem. Bioenerg. 47, 179-183. (1998)


Apoflavodoxin: Structure, stability, and FMN binding. 

Maldonado, S., Lostao, A., Irún, M.P., Fernández-Recio, J., Genzor, C.G., González, E.B., Rubio, J.A., Luquita, A., Daoudi, F., Sancho, J.

Biochimie 80, 813-820. (1998)


Intrahelical side chain interactions in a-helices: poor correlation between energetics and frequency.

Fernández-Recio, J., Sancho, J.

FEBS Lett. 429, 99-103. (1998)


The tryptophan/histidine interaction in a-helices.

Fernández-Recio, J., Vázquez, A., Civera, C., Sevilla, P., Sancho, J.

J. Mol. Biol. 267, 184-197. (1997)

 


Project Funding

Ongoing Projects


Reference: BIO2016-79930-R

Title: Improving structural and energetics modeling of protein interactions for the new challenges in biomedicine

Total awarded: €150,000 (1.1.2017-31.12.2019)

Role: PI

I+D+i, Ministry of Economy, Industry and Competitivity


Reference: PIREPRED

Title: Red transfronteriza de interpretación del cribado neonatal: de la mutación al paciente.

Total awarded: €155,542 (1.1.2016-31.12.2019)

Role: co-PI

INTERREG V A España-Francia-Andorra (POCTEFA)


Reference: 676556 MuG

Title: Multi-scale complex genomics

Total awarded: €475,000 (1.1.2015-31.12.2018)

Role: co-PI

European Comission EINFRA-9-2015 H2020


Title: Identification and characterization of LAT2 inhibitors

Total awarded: €132,000 (1.1.2016-31.12.2018)

Role: co-PI

SIDRA Medidal and Research Center (Qatar Fundation)


Project Funding

Concluded Projects

(last 5 years)


Reference: BIO2014-57314-REDT

Title: Comprensión, predicción y validación del fenotipo de las mutaciones patológicas: transformándolos resultados básicos en herramientas de diagnóstico.

Total awarded: €25,000 (1.1.2014 – 31.12.2016)

Role: Co-PI

Ministry of Economy and Competitivity


Reference: BIO2013-48213-R

Title: New methodological developements in protein-protein docking forthe challenges of interactomics and personalized medicine

Total awarded: €155,000 (1.1.2014 – 31.12.2016)

Role: PI

Ministry of Economy and Competitivity


Reference: 2014SGR9

Title: Structure-based discovery of new inhibitors of the glutmate transporter xCT for the treatment of human gliomas

Total awarded: €135,625 (2014 – 2016)

Role: PI

Fundació La Marató TV3


Reference: BIO2013-49320-EXP

Title: Protein docking and beyond: imroving biophysical and computational description of protein-protein and protein-RNA interactions

Total awarded: €160,000 (2011-2013)

Role: PI

Ministry of Economy and Competitivity


Vacancies/Jobs

INPhINIT 2018 J. Fernández Recio Position

Rational design of small-molecule inhibitors of amino acid transmembrane transporters for drug discovery   INPhINIT,…

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