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Fleishman, S. J., Whitehead, T. A., Strauch, E.-M., Corn, J. E., Qin, S., Zhou, H.-X., Mitchell, J. C., Demerdash, O. N. A., Takeda-Shitaka, M., Terashi, G., Moal, I. H., Li, X., Bates, P. A., Zacharias, M., Park, H., Ko, J., Lee, H., Seok, C., Bourquard, T., … Baker, D. (2011). Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology. Journal of Molecular Biology, 414(2), 289–302. https://doi.org/10.1016/j.jmb.2011.09.031

Fernández-Recio, J., & Verma, C. (2010). Theory and simulation: integrating models into experimental scenarios. Current Opinion in Structural Biology, 20(2), 139–141. https://doi.org/10.1016/j.sbi.2010.02.002

Fernández‐Recio, J., & Sternberg, M. J. E. (2010). The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona. Proteins: Structure, Function, and Bioinformatics, 78(15), 3065–3066. Portico. https://doi.org/10.1002/prot.22801

Pons, C., D’Abramo, M., Svergun, D. I., Orozco, M., Bernadó, P., & Fernández-Recio, J. (2010). Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data. Journal of Molecular Biology, 403(2), 217–230. https://doi.org/10.1016/j.jmb.2010.08.029

Solernou, A., & Fernandez-Recio, J. (2010). Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-352

Pons, C., Solernou, A., Perez‐Cano, L., Grosdidier, S., & Fernandez‐Recio, J. (2010). Optimization of pyDock for the new CAPRI challenges: Docking of homology‐based models, domain–domain assembly and protein‐RNA binding. Proteins: Structure, Function, and Bioinformatics, 78(15), 3182–3188. Portico. https://doi.org/10.1002/prot.22773

Eliahoo, E., Ben Yosef, R., Pérez-Cano, L., Fernández-Recio, J., Glaser, F., & Manor, H. (2010). Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study. Nucleic Acids Research, 38(9), 2975–2989. https://doi.org/10.1093/nar/gkp1230

Valdés, H., Díaz, N., Suárez, D., & Fernández-Recio, J. (2010). Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein−Protein Docking Calculations Using pyDock. Journal of Chemical Theory and Computation, 6(7), 2204–2213. https://doi.org/10.1021/ct100097x

Alías, M., Ayuso-Tejedor, S., Fernández-Recio, J., Cativiela, C., & Sancho, J. (2010). Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine. Organic & Biomolecular Chemistry, 8(4), 788. https://doi.org/10.1039/b919671d

Kurzak, J., Bader, D. A., & Dongarra, J. (Eds.). (2010). Scientific Computing with Multicore and Accelerators. https://doi.org/10.1201/b10376

Pérez-Cano, L., & Fernández-Recio, J. (2010). Dissection and prediction of RNA-binding sites on proteins. Bmc, 1(5–6), 345–355. https://doi.org/10.1515/bmc.2010.037

Bernadó, P., Pérez, Y., Blobel, J., Fernández‐Recio, J., Svergun, D. I., & Pons, M. (2009). Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small‐angle X‐ray scattering. Protein Science, 18(4), 716–726. Portico. https://doi.org/10.1002/pro.83

Mosca, R., Pons, C., Fernández-Recio, J., & Aloy, P. (2009). Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments. PLoS Computational Biology, 5(8), e1000490. https://doi.org/10.1371/journal.pcbi.1000490

Arafat, Y., Kamruzzaman, J., Karmakar, G. C., & Recio, J. F. (2009). Predicting protein protein interfaces as clusters of Optimal Docking Area points. International Journal of Data Mining and Bioinformatics, 3(1), 55. https://doi.org/10.1504/ijdmb.2009.023884

Casasoli, M., Federici, L., Spinelli, F., Di Matteo, A., Vella, N., Scaloni, F., Fernandez-Recio, J., Cervone, F., & De Lorenzo, G. (2009). Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein. Proceedings of the National Academy of Sciences, 106(18), 7666–7671. https://doi.org/10.1073/pnas.0812625106

Grosdidier, S., & Fernández-Recio, J. (2009). Docking and scoring: applications to drug discovery in the interactomics era. Expert Opinion on Drug Discovery, 4(6), 673–686. https://doi.org/10.1517/17460440903002067

Pons, C., Grosdidier, S., Solernou, A., Pérez‐Cano, L., & Fernández‐Recio, J. (2009). Present and future challenges and limitations in protein–protein docking. Proteins: Structure, Function, and Bioinformatics, 78(1), 95–108. Portico. https://doi.org/10.1002/prot.22564

Pérez‐Cano, L., & Fernández‐Recio, J. (2009). Optimal protein‐RNA area, OPRA: A propensity‐based method to identify RNA‐binding sites on proteins. Proteins: Structure, Function, and Bioinformatics, 78(1), 25–35. Portico. https://doi.org/10.1002/prot.22527

Garzon, J. I., Lopéz-Blanco, J. R., Pons, C., Kovacs, J., Abagyan, R., Fernandez-Recio, J., & Chacon, P. (2009). FRODOCK: a new approach for fast rotational protein–protein docking. Bioinformatics, 25(19), 2544–2551. https://doi.org/10.1093/bioinformatics/btp447

Cheng, T. M., Blundell, T. L., & Fernandez-Recio, J. (2008). Structural assembly of two-domain proteins by rigid-body docking. BMC Bioinformatics, 9(1). https://doi.org/10.1186/1471-2105-9-441

Degryse, B., Fernandez-Recio, J., Citro, V., Blasi, F., & Cubellis, M. V. (2008). In silico docking of urokinase plasminogen activator and integrins. BMC Bioinformatics, 9(S2). https://doi.org/10.1186/1471-2105-9-s2-s8

Grosdidier, S., & Fernández-Recio, J. (2008). Identification of hot-spot residues in protein-protein interactions by computational docking. BMC Bioinformatics, 9(1). https://doi.org/10.1186/1471-2105-9-447

Fernández-Recio, J., & Verma, C. (2008). Editorial. Current Opinion in Structural Biology, 18(2), 131–133. https://doi.org/10.1016/j.sbi.2008.03.001

Hart, S. E., Howe, C. J., Mizuguchi, K., & Fernandez-Recio, J. (2008). Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum. Protein Engineering, Design and Selection, 21(12), 689–698. https://doi.org/10.1093/protein/gzn051

Medina, M., Abagyan, R., Gómez‐Moreno, C., & Fernandez‐Recio, J. (2008). Docking analysis of transient complexes: Interaction of ferredoxin‐NADP+ reductase with ferredoxin and flavodoxin. Proteins: Structure, Function, and Bioinformatics, 72(3), 848–862. Portico. https://doi.org/10.1002/prot.21979

Pallarès, I., Fernández, D., Comellas-Bigler, M., Fernández-Recio, J., Ventura, S., Avilés, F. X., Bode, W., & Vendrell, J. (2008). Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid). Acta Crystallographica Section D Biological Crystallography, 64(7), 784–791. https://doi.org/10.1107/s0907444908013474

Bavro, V. N., Pietras, Z., Furnham, N., Pérez-Cano, L., Fernández-Recio, J., Pei, X. Y., Misra, R., & Luisi, B. (2008). Assembly and Channel Opening in a Bacterial Drug Efflux Machine. Molecular Cell, 30(1), 114–121. https://doi.org/10.1016/j.molcel.2008.02.015

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. (2007). The Structure of Human 4F2hc Ectodomain Provides a Model for Homodimerization and Electrostatic Interaction with Plasma Membrane. Journal of Biological Chemistry, 282(43), 31444–31452. https://doi.org/10.1074/jbc.m704524200

Fernández, D., Vendrell, J., Avilés, F. X., & Fernández‐Recio, J. (2007). Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis. Proteins: Structure, Function, and Bioinformatics, 68(1), 131–144. Portico. https://doi.org/10.1002/prot.21390

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. (2007). Recognition and Cooperation Between the ATP-dependent RNA Helicase RhlB and Ribonuclease RNase E. Journal of Molecular Biology, 367(1), 113–132. https://doi.org/10.1016/j.jmb.2006.12.014

Cheng, T. M., Blundell, T. L., & Fernandez‐Recio, J. (2007). pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking. Proteins: Structure, Function, and Bioinformatics, 68(2), 503–515. Portico. https://doi.org/10.1002/prot.21419

Grosdidier, S., Pons, C., Solernou, A., & Fernández‐Recio, J. (2007). Prediction and scoring of docking poses with pyDock. Proteins: Structure, Function, and Bioinformatics, 69(4), 852–858. Portico. https://doi.org/10.1002/prot.21796

Bonivento, D., Pontiggia, D., Matteo, A. D., Fernandez‐Recio, J., Salvi, G., Tsernoglou, D., Cervone, F., Lorenzo, G. D., & Federici, L. (2007). Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase‐inhibiting proteins. Proteins: Structure, Function, and Bioinformatics, 70(1), 294–299. Portico. https://doi.org/10.1002/prot.21610

Arafat, Y., Karmakar, G. C., Kamruzzaman, J., & Fernandez-Recio, J. (2006). Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching. 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, 1–8. https://doi.org/10.1109/cibcb.2006.331004

Federici, L., Di Matteo, A., Fernandez-Recio, J., Tsernoglou, D., & Cervone, F. (2006). Polygalacturonase inhibiting proteins: players in plant innate immunity? Trends in Plant Science, 11(2), 65–70. https://doi.org/10.1016/j.tplants.2005.12.005

Yraola, F., García-Vicente, S., Fernández-Recio, J., Albericio, F., Zorzano, A., Marti, L., & Royo, M. (2006). New Efficient Substrates for Semicarbazide-Sensitive Amine Oxidase/VAP-1 Enzyme:  Analysis by SARs and Computational Docking. Journal of Medicinal Chemistry, 49(21), 6197–6208. https://doi.org/10.1021/jm051076e

Bolanos-Garcia, V. M., Fernandez-Recio, J., Allende, J. E., & Blundell, T. L. (2006). Identifying interaction motifs in CK2β – a ubiquitous kinase regulatory subunit. Trends in Biochemical Sciences, 31(12), 654–661. https://doi.org/10.1016/j.tibs.2006.10.005

Chelliah, V., Blundell, T. L., & Fernández-Recio, J. (2006). Efficient Restraints for Protein–Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment. Journal of Molecular Biology, 357(5), 1669–1682. https://doi.org/10.1016/j.jmb.2006.01.001

Orozco, M., Noy, A., Meyer, T., Rueda, M., Ferrer, C., Valencia, A., Pérez, A., Carrillo, O., Fernandez-Recio, J., de la Cruz, X., & Luque, F. J. (2006). Data Mining of Molecular Dynamic Trajectories of Nucleic Acids. Computational Studies of RNA and DNA, 121–145. https://doi.org/10.1007/978-1-4020-4851-3_5

Blundell, T. L., & Fernández-Recio, J. (2006). Brief encounters bolster contacts. Nature, 444(7117), 279–280. https://doi.org/10.1038/nature05306

Sicilia, F., Fernandez-Recio, J., Caprari, C., De Lorenzo, G., Tsernoglou, D., Cervone, F., & Federici, L. (2005). The Polygalacturonase-Inhibiting Protein PGIP2 of Phaseolus vulgaris Has Evolved a Mixed Mode of Inhibition of Endopolygalacturonase PG1 of Botrytis cinerea. Plant Physiology, 139(3), 1380–1388. https://doi.org/10.1104/pp.105.067546

Federici, L., Du, D., Walas, F., Matsumura, H., Fernandez-Recio, J., McKeegan, K. S., Borges-Walmsley, M. I., Luisi, B. F., & Walmsley, A. R. (2005). The Crystal Structure of the Outer Membrane Protein VceC from the Bacterial Pathogen Vibrio cholerae at 1.8 Å Resolution. Journal of Biological Chemistry, 280(15), 15307–15314. https://doi.org/10.1074/jbc.m500401200

Fernández‐Recio, J., Abagyan, R., & Totrov, M. (2005). Improving CAPRI predictions: Optimized desolvation for rigid‐body docking. Proteins: Structure, Function, and Bioinformatics, 60(2), 308–313. Portico. https://doi.org/10.1002/prot.20575

López-Llano, J., Maldonado, S., Jain, S., Lostao, A., Godoy-Ruiz, R., Sanchez-Ruiz, J. M., Cortijo, M., Fernández-Recio, J., & Sancho, J. (2004). The Long and Short Flavodoxins. Journal of Biological Chemistry, 279(45), 47184–47191. https://doi.org/10.1074/jbc.m405791200

Fernandez-Recio, J., Walas, F., Federici, L., Venkatesh Pratap, J., Bavro, V. N., Miguel, R. N., Mizuguchi, K., & Luisi, B. (2004). A model of a transmembrane drug‐efflux pump from Gram‐negative bacteria. FEBS Letters, 578(1–2), 5–9. Portico. https://doi.org/10.1016/j.febslet.2004.10.097

Fernandez‐Recio, J., Totrov, M., Skorodumov, C., & Abagyan, R. (2004). Optimal docking area: A new method for predicting protein–protein interaction sites. Proteins: Structure, Function, and Bioinformatics, 58(1), 134–143. Portico. https://doi.org/10.1002/prot.20285

Fernández‐Recio, J., Totrov, M., & Abagyan, R. (2003). ICM‐DISCO docking by global energy optimization with fully flexible side‐chains. Proteins: Structure, Function, and Bioinformatics, 52(1), 113–117. Portico. https://doi.org/10.1002/prot.10383

Harmer, N. J., Pellegrini, L., Chirgadze, D., Fernandez-Recio, J., & Blundell, T. L. (2003). 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,. Biochemistry, 43(3), 629–640. https://doi.org/10.1021/bi035320k

Fernández‐Recio, J., Totrov, M., & Abagyan, R. (2002). Soft protein–protein docking in internal coordinates. Protein Science, 11(2), 280–291. Portico. https://doi.org/10.1110/ps.19202

Fernández-Recio, J., Genzor, C. G., & Sancho, J. (2001). Apoflavodoxin Folding Mechanism:  An α/β Protein with an Essentially Off-Pathway Intermediate. Biochemistry, 40(50), 15234–15245. https://doi.org/10.1021/bi010216t

Madoz-Gúrpide, J., Abad, J. M., Fernández-Recio, J., Vélez, M., Vázquez, L., Gómez-Moreno, C., & Fernández, V. M. (2000). Modulation of Electroenzymatic NADPH Oxidation through Oriented Immobilization of Ferredoxin:NADP+ Reductase onto Modified Gold Electrodes. Journal of the American Chemical Society, 122(40), 9808–9817. https://doi.org/10.1021/ja001365m

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Maldonado, S., Lostao, A., Irún, M. P., Férnandez-Recio, J., Genzor, C. G., González, E. B., Rubio, J. A., Luquita, A., Daoudi, F., & Sancho, J. (1998). Apoflavodoxin: Structure, stability, and FMN binding. Biochimie, 80(10), 813–820. https://doi.org/10.1016/s0300-9084(00)88876-8

Fernández-Recio, J., Vázquez, A., Civera, C., Sevilla, P., & Sancho, J. (1997). The Tryptophan/Histidine interaction in α-helices. Journal of Molecular Biology, 267(1), 184–197. https://doi.org/10.1006/jmbi.1996.0831

Fernández-Recio, J., Vázquez, A., Civera, C., Sevilla, P., & Sancho, J. (1997). The tryptophan/histidine interaction in α-helices. Journal of Molecular Biology, 270(3), 535. https://doi.org/10.1006/jmbi.1997.1117