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Juan Fernandez-Recio - Publications

Affiliations: 
2007-2017 Life Sciences Barcelona Supercomputing Center, Barcelona, Catalunya, Spain 
 2017-2019 Institut de Biologia Molecular de Barcelona Consejo Superior de Investigaciones Científicas 
 2019- Instituto de Ciencias de la Vid y del Vino (ICVV) Consejo Superior de Investigaciones Científicas 
Area:
Computational Biology, Molecular Modeling, Protein Structure and Interactions, Protein-protein Docking
Website:
https://www.icvv.es/english/3dbiowine
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125 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Venezian J, Bar-Yosef H, Ben-Arie Zilberman H, Cohen N, Kleifeld O, Fernandez-Recio J, Glaser F, Shiber A. Diverging co-translational protein complex assembly pathways are governed by interface energy distribution. Nature Communications. 15: 2638. PMID 38528060 DOI: 10.1038/s41467-024-46881-w  0.361
2024 Erausquin E, Rodríguez-Fernández A, Rodríguez-Lumbreras LÁ, Fernández-Recio J, Dichiara-Rodríguez MG, López-Sagaseta J. Structural vulnerability in EPCR suggests functional modulation. Scientific Reports. 14: 2591. PMID 38297105 DOI: 10.1038/s41598-024-53160-7  0.823
2023 Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, ... ... Fernandez-Recio J, et al. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins. PMID 37905971 DOI: 10.1002/prot.26609  0.842
2023 Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LA, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin AMJJ, Savojardo C, et al. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics. e2200323. PMID 37365936 DOI: 10.1002/pmic.202200323  0.841
2023 Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nature Structural & Molecular Biology. PMID 37322239 DOI: 10.1038/s41594-023-01014-7  0.774
2022 Rodríguez-Lumbreras LA, Jiménez-García B, Giménez-Santamarina S, Fernández-Recio J. pyDockDNA: A new web server for energy-based protein-DNA docking and scoring. Frontiers in Molecular Biosciences. 9: 988996. PMID 36275623 DOI: 10.3389/fmolb.2022.988996  0.828
2022 Erausquin E, Glaser F, Fernández-Recio J, López-Sagaseta J. Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution. Acta Crystallographica. Section D, Structural Biology. 78: 1156-1170. PMID 36048155 DOI: 10.1107/S2059798322007677  0.426
2022 Landras A, Reger de Moura C, Villoutreix BO, Battistella M, Sadoux A, Dumaz N, Menashi S, Fernández-Recio J, Lebbé C, Mourah S. Novel treatment strategy for NRAS-mutated melanoma through a selective inhibitor of CD147/VEGFR-2 interaction. Oncogene. 41: 2254-2264. PMID 35217792 DOI: 10.1038/s41388-022-02244-7  0.265
2022 Galano-Frutos JJ, García-Cebollada H, López A, Rosell M, Cruz X, Fernández-Recio J, Sancho J. PirePred: An Accurate Online Consensus Tool to Interpret Newborn Screening-Related Genetic Variants in Structural Context. The Journal of Molecular Diagnostics : Jmd. PMID 35143952 DOI: 10.1016/j.jmoldx.2022.01.005  0.807
2021 Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, ... ... Fernandez-Recio J, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. PMID 34453465 DOI: 10.1002/prot.26222  0.828
2021 Castell C, Rodríguez-Lumbreras LA, Hervás M, Fernández-Recio J, Navarro JA. 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 & Cell Physiology. PMID 33772595 DOI: 10.1093/pcp/pcab044  0.8
2021 Rosell M, Rodríguez-Lumbreras LA, Fernández-Recio J. Modeling of Protein Complexes and Molecular Assemblies with pyDock. Methods in Molecular Biology (Clifton, N.J.). 2165: 175-198. PMID 32621225 DOI: 10.1007/978-1-0716-0708-4_10  0.862
2021 Elorza-Vidal X, Xicoy-Espaulella E, Pla-Casillanis A, Alonso-Gardón M, Gaitán-Peñas H, Engel-Pizcueta C, Fernández-Recio J, Estévez R. Structural basis for the dominant or recessive character of GLIALCAM mutations found in leukodystrophies. Human Molecular Genetics. 29: 1107-1120. PMID 31960914 DOI: 10.1093/hmg/ddaa009  0.349
2020 Rosell M, Fernández-Recio J. Docking-based identification of small-molecule binding sites at protein-protein interfaces. Computational and Structural Biotechnology Journal. 18: 3750-3761. PMID 33250973 DOI: 10.1016/j.csbj.2020.11.029  0.874
2020 Amengual-Rigo P, Fernández-Recio J, Guallar V. UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. Bioinformatics (Oxford, England). PMID 32761082 DOI: 10.1093/Bioinformatics/Btaa708  0.545
2020 Rosell M, Fernández-Recio J. Docking approaches for modeling multi-molecular assemblies. Current Opinion in Structural Biology. 64: 59-65. PMID 32615514 DOI: 10.1016/j.sbi.2020.05.016  0.841
2020 Fernández-Recio J. Modelling the Evolution of COVID-19 in High-Incidence European Countries and Regions: Estimated Number of Infections and Impact of Past and Future Intervention Measures. Journal of Clinical Medicine. 9. PMID 32545264 DOI: 10.3390/jcm9061825  0.264
2020 Jiménez-García B, Bernadó P, Fernández-Recio J. Structural Characterization of Protein-Protein Interactions with pyDockSAXS. Methods in Molecular Biology (Clifton, N.J.). 2112: 131-144. PMID 32006283 DOI: 10.1007/978-1-0716-0270-6_10  0.569
2020 Romero-Durana M, Jiménez-García B, Fernández-Recio J. pyDockEneRes: per-residue decomposition of protein-protein docking energy. Bioinformatics (Oxford, England). 36: 2284-2285. PMID 31808797 DOI: 10.1093/bioinformatics/btz884  0.871
2019 Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Jiménez-García B, Díaz L, Fernández-Recio J. Integrative modeling of protein-protein interactions with pyDock for the new docking challenges. Proteins. PMID 31746039 DOI: 10.1002/prot.25858  0.842
2019 Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Fernandez-Recio J, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  0.802
2019 Errasti-Murugarren E, Fort J, Bartoccioni P, Díaz L, Pardon E, Carpena X, Espino-Guarch M, Zorzano A, Ziegler C, Steyaert J, Fernández-Recio J, Fita I, Palacín M. L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction. Nature Communications. 10: 1807. PMID 31000719 DOI: 10.1038/s41467-019-09837-z  0.305
2019 Navío D, Rosell M, Aguirre J, de la Cruz X, Fernández-Recio J. Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. International Journal of Molecular Sciences. 20. PMID 30934865 DOI: 10.3390/ijms20071583  0.842
2019 Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics (Oxford, England). 35: 462-469. PMID 30020414 DOI: 10.1093/bioinformatics/bty635  0.787
2018 Ordan M, Pallara C, Maik-Rachline G, Hanoch T, Gervasio FL, Glaser F, Fernandez-Recio J, Seger R. Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases. Scientific Reports. 8: 11830. PMID 30087384 DOI: 10.1038/S41598-018-30202-5  0.766
2018 Rosell M, Fernández-Recio J. Hot-spot analysis for drug discovery targeting protein-protein interactions. Expert Opinion On Drug Discovery. 13: 327-338. PMID 29376444 DOI: 10.1080/17460441.2018.1430763  0.868
2018 Jiménez-García B, Roel-Touris J, Romero-Durana M, Vidal M, Jiménez-González D, Fernández-Recio J. LightDock: a new multi-scale approach to protein-protein docking. Bioinformatics (Oxford, England). 34: 49-55. PMID 28968719 DOI: 10.1093/bioinformatics/btx555  0.866
2017 Barradas-Bautista D, Rosell M, Pallara C, Fernández-Recio J. Structural Prediction of Protein-Protein Interactions by Docking: Application to Biomedical Problems. Advances in Protein Chemistry and Structural Biology. 110: 203-249. PMID 29412997 DOI: 10.1016/bs.apcsb.2017.06.003  0.856
2017 Garcia-Pardo J, Tanco S, Díaz L, Dasgupta S, Fernandez-Recio J, Lorenzo J, Aviles FX, Fricker LD. Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains. Plos One. 12: e0187778. PMID 29131831 DOI: 10.1371/journal.pone.0187778  0.275
2017 Barradas-Bautista D, Fernández-Recio J. Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations. Plos One. 12: e0183643. PMID 28841721 DOI: 10.1371/journal.pone.0183643  0.54
2017 Barradas-Bautista D, Moal IH, Fernández-Recio J. A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining. Proteins. 85: 1287-1297. PMID 28342242 DOI: 10.1002/prot.25289  0.815
2017 Moal IH, Barradas-Bautista D, Jiménez-García B, Torchala M, van der Velde A, Vreven T, Weng Z, Bates PA, Fernández-Recio J. IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection. Bioinformatics (Oxford, England). PMID 28200016 DOI: 10.1093/Bioinformatics/Btx068  0.784
2017 Romero-Durana M, Pallara C, Glaser F, Fernández-Recio J. Modeling Binding Affinity of Pathological Mutations for Computational Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 139-159. PMID 27914049 DOI: 10.1007/978-1-4939-6637-0_6  0.86
2016 Pérez-Cano L, Romero-Durana M, Fernández-Recio J. Structural and energy determinants in protein-RNA docking. Methods (San Diego, Calif.). 163-170. PMID 27816523 DOI: 10.1016/j.ymeth.2016.11.001  0.849
2016 Pallara C, Jiménez-García B, Romero M, Moal IH, Fernández-Recio J. pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions. Proteins. 85: 487-496. PMID 27701776 DOI: 10.1002/prot.25184  0.847
2016 Agostino M, Mancera RL, Ramsland PA, Fernández-Recio J. Optimization of protein-protein docking for predicting Fc-protein interactions. Journal of Molecular Recognition : Jmr. PMID 27445195 DOI: 10.1002/jmr.2555  0.859
2016 Fernández-Recio J. Unraveling the molecular details of the innate immune response. Ebiomedicine. 9: 7-8. PMID 27374315 DOI: 10.1016/j.ebiom.2016.06.025  0.194
2016 Pallara C, Rueda M, Abagyan R, Fernández-Recio J. Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters. Journal of Chemical Theory and Computation. 12: 3236-49. PMID 27294484 DOI: 10.1021/Acs.Jctc.6B00204  0.865
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.849
2016 Khayati F, Pérez-Cano L, Maouche K, Sadoux A, Boutalbi Z, Podgorniak MP, Maskos U, Setterblad N, Janin A, Calvo F, Lebbé C, Menashi S, Fernandez-Recio J, Mourah S. EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGF. Oncotarget. 6: 9766-80. PMID 25825981 DOI: 10.18632/oncotarget.2870  0.743
2015 Bernal-Bayard P, Pallara C, Carmen Castell M, Molina-Heredia FP, Fernández-Recio J, Hervás M, Navarro JA. Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor. Biochimica Et Biophysica Acta. 1847: 1549-59. PMID 26407632 DOI: 10.1016/j.bbabio.2015.09.006  0.756
2015 Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology. 427: 3031-41. PMID 26231283 DOI: 10.1016/J.Jmb.2015.07.016  0.855
2015 Pérez-Cano L, Fernández-Recio J. Dissection and prediction of RNA-binding sites on proteins. Biomolecular Concepts. 1: 345-55. PMID 25962008 DOI: 10.1515/bmc.2010.037  0.795
2015 Jiménez-García B, Pons C, Svergun DI, Bernadó P, Fernández-Recio J. pyDockSAXS: protein-protein complex structure by SAXS and computational docking. Nucleic Acids Research. 43: W356-61. PMID 25897115 DOI: 10.1093/Nar/Gkv368  0.671
2015 Somajo S, Ahnström J, Fernandez-Recio J, Gierula M, Villoutreix BO, Dahlbäck B. Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction. Thrombosis and Haemostasis. 113: 976-87. PMID 25716664 DOI: 10.1160/Th14-09-0803  0.468
2015 Moal IH, Dapkūnas J, Fernández-Recio J. Inferring the microscopic surface energy of protein-protein interfaces from mutation data. Proteins. 83: 640-50. PMID 25586563 DOI: 10.1002/prot.24761  0.748
2014 Moal IH, Fernández-Recio J. Comment on 'protein-protein binding affinity prediction from amino acid sequence'. Bioinformatics (Oxford, England). 31: 614-5. PMID 25381451 DOI: 10.1093/bioinformatics/btu682  0.777
2014 Moal IH, Jiménez-García B, Fernández-Recio J. CCharPPI web server: computational characterization of protein-protein interactions from structure. Bioinformatics (Oxford, England). 31: 123-5. PMID 25183488 DOI: 10.1093/bioinformatics/btu594  0.797
2014 Lucas M, Gaspar AH, Pallara C, Rojas AL, Fernández-Recio J, Machner MP, Hierro A. Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5. Proceedings of the National Academy of Sciences of the United States of America. 111: E3514-23. PMID 25114243 DOI: 10.1073/Pnas.1405391111  0.82
2014 Lang V, Pallara C, Zabala A, Lobato-Gil S, Lopitz-Otsoa F, Farrás R, Hjerpe R, Torres-Ramos M, Zabaleta L, Blattner C, Hay RT, Barrio R, Carracedo A, Fernandez-Recio J, Rodríguez MS, et al. Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity. Molecular Oncology. 8: 1026-42. PMID 24816189 DOI: 10.1016/j.molonc.2014.04.002  0.754
2014 Rosell A, Meury M, Álvarez-Marimon E, Costa M, Pérez-Cano L, Zorzano A, Fernández-Recio J, Palacín M, Fotiadis D. Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc. Proceedings of the National Academy of Sciences of the United States of America. 111: 2966-71. PMID 24516142 DOI: 10.1073/pnas.1323779111  0.76
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.812
2013 Emperador A, Solernou A, Sfriso P, Pons C, Gelpi JL, Fernandez-Recio J, Orozco M. Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 9: 1222-9. PMID 26588765 DOI: 10.1021/ct301039e  0.863
2013 Pons C, Fenwick RB, Esteban-Martín S, Salvatella X, Fernandez-Recio J. Validated Conformational Ensembles Are Key for the Successful Prediction of Protein Complexes. Journal of Chemical Theory and Computation. 9: 1830-7. PMID 26587639 DOI: 10.1021/ct300990h  0.794
2013 Moal IH, Fernandez-Recio J. Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation. Journal of Chemical Theory and Computation. 9: 3715-27. PMID 26584123 DOI: 10.1021/ct400295z  0.803
2013 Moal IH, Torchala M, Bates PA, Fernández-Recio J. The scoring of poses in protein-protein docking: current capabilities and future directions. Bmc Bioinformatics. 14: 286. PMID 24079540 DOI: 10.1186/1471-2105-14-286  0.818
2013 Agius R, Torchala M, Moal IH, Fernández-Recio J, Bates PA. Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization. Plos Computational Biology. 9: e1003216. PMID 24039569 DOI: 10.1371/journal.pcbi.1003216  0.746
2013 Pérez-Cano L, Eliahoo E, Lasker K, Wolfson HJ, Glaser F, Manor H, Bernadó P, Fernández-Recio J. Conformational transitions in human translin enable nucleic acid binding. Nucleic Acids Research. 41: 9956-66. PMID 23980029 DOI: 10.1093/Nar/Gkt765  0.782
2013 Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Proteins. 81: 2192-200. PMID 23934865 DOI: 10.1002/prot.24387  0.834
2013 Moal IH, Moretti R, Baker D, Fernández-Recio J. Scoring functions for protein-protein interactions. Current Opinion in Structural Biology. 23: 862-7. PMID 23871100 DOI: 10.1016/J.Sbi.2013.06.017  0.812
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Fernandez-Recio J, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.817
2013 Chen Y, Tascón I, Neunuebel MR, Pallara C, Brady J, Kinch LN, Fernández-Recio J, Rojas AL, Machner MP, Hierro A. Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD. Plos Pathogens. 9: e1003382. PMID 23696742 DOI: 10.1371/Journal.Ppat.1003382  0.821
2013 Jiménez-García B, Pons C, Fernández-Recio J. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics (Oxford, England). 29: 1698-9. PMID 23661696 DOI: 10.1093/bioinformatics/btt262  0.785
2013 Grosdidier S, Fernández-Recio J. Docking and scoring: applications to drug discovery in the interactomics era. Expert Opinion On Drug Discovery. 4: 673-86. PMID 23489159 DOI: 10.1517/17460440903002067  0.809
2013 Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA. SwarmDock: a server for flexible protein-protein docking. Bioinformatics (Oxford, England). 29: 807-9. PMID 23343604 DOI: 10.1093/bioinformatics/btt038  0.809
2013 Grosdidier S, Fernández-Recio J. Protein-protein docking and hot-spot prediction for drug discovery. Current Pharmaceutical Design. 18: 4607-18. PMID 22650255 DOI: 10.2174/138161212802651599  0.86
2013 Pérez-Cano L, Solernou A, Pons C, Fernández-Recio J. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 293-301. PMID 19908381 DOI: 10.1142/9789814295291_0031  0.823
2012 Moal IH, Fernández-Recio J. SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models. Bioinformatics (Oxford, England). 28: 2600-7. PMID 22859501 DOI: 10.1093/bioinformatics/bts489  0.802
2012 Pons C, Jiménez-González D, González-Álvarez C, Servat H, Cabrera-Benítez D, Aguilar X, Fernández-Recio J. Cell-Dock: high-performance protein-protein docking. Bioinformatics (Oxford, England). 28: 2394-6. PMID 22815362 DOI: 10.1093/bioinformatics/bts454  0.722
2012 Grosdidier S, Carbó LR, Buzón V, Brooke G, Nguyen P, Baxter JD, Bevan C, Webb P, Estébanez-Perpiñá E, Fernández-Recio J. Allosteric conversation in the androgen receptor ligand-binding domain surfaces Molecular Endocrinology. 26: 1078-1090. PMID 22653923 DOI: 10.1210/Me.2011-1281  0.779
2012 Pérez-Cano L, Jiménez-García B, Fernández-Recio J. A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins. 80: 1872-82. PMID 22488990 DOI: 10.1002/prot.24075  0.794
2012 Fernandez-Recio J, Verma C. Theory and simulation: complexity and emergence. Current Opinion in Structural Biology. 22: 127-9. PMID 22417973 DOI: 10.1016/J.Sbi.2012.02.002  0.228
2012 Taboureau O, Baell JB, Fernández-Recio J, Villoutreix BO. Established and emerging trends in computational drug discovery in the structural genomics era. Chemistry & Biology. 19: 29-41. PMID 22284352 DOI: 10.1016/j.chembiol.2011.12.007  0.379
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.825
2011 Pons C, Glaser F, Fernandez-Recio J. Prediction of protein-binding areas by small-world residue networks and application to docking. Bmc Bioinformatics. 12: 378. PMID 21943333 DOI: 10.1186/1471-2105-12-378  0.803
2011 Helft L, Reddy V, Chen X, Koller T, Federici L, Fernández-Recio J, Gupta R, Bent A. LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains. Plos One. 6: e21614. PMID 21789174 DOI: 10.1371/Journal.Pone.0021614  0.528
2011 Solernou A, Fernandez-Recio J. pyDockCG: new coarse-grained potential for protein-protein docking. The Journal of Physical Chemistry. B. 115: 6032-9. PMID 21506617 DOI: 10.1021/jp112292b  0.86
2011 Pons C, Talavera D, de la Cruz X, Orozco M, Fernandez-Recio J. Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking. Journal of Chemical Information and Modeling. 51: 370-7. PMID 21214199 DOI: 10.1021/Ci100353E  0.817
2011 Pons C, Solernou A, Perez-Cano L, Grosdidier S, Fernandez-Recio J. Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins. 78: 3182-8. PMID 20602351 DOI: 10.1002/prot.22773  0.798
2010 Valdés H, Díaz N, Suárez D, Fernández-Recio J. Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein-Protein Docking Calculations Using pyDock. Journal of Chemical Theory and Computation. 6: 2204-13. PMID 26615946 DOI: 10.1021/ct100097x  0.359
2010 Pons C, D'Abramo M, Svergun DI, Orozco M, Bernadó P, Fernández-Recio J. Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. Journal of Molecular Biology. 403: 217-30. PMID 20804770 DOI: 10.1016/J.Jmb.2010.08.029  0.805
2010 Solernou A, Fernandez-Recio J. Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. Bmc Bioinformatics. 11: 352. PMID 20584304 DOI: 10.1186/1471-2105-11-352  0.854
2010 Fernández-Recio J, Verma C. Theory and simulation: integrating models into experimental scenarios. Current Opinion in Structural Biology. 20: 139-41. PMID 20226653 DOI: 10.1016/J.Sbi.2010.02.002  0.242
2010 Alías M, Ayuso-Tejedor S, Fernández-Recio J, Cativiela C, Sancho J. Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine Organic and Biomolecular Chemistry. 8: 788-792. PMID 20135035 DOI: 10.1039/B919671D  0.627
2010 Eliahoo E, Ben Yosef R, Pérez-Cano L, Fernández-Recio J, Glaser F, Manor H. 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: 2975-89. PMID 20081200 DOI: 10.1093/Nar/Gkp1230  0.835
2010 Pons C, Grosdidier S, Solernou A, Pérez-Cano L, Fernández-Recio J. Present and future challenges and limitations in protein-protein docking. Proteins. 78: 95-108. PMID 19731373 DOI: 10.1002/prot.22564  0.856
2010 Pérez-Cano L, Fernández-Recio J. Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins. 78: 25-35. PMID 19714772 DOI: 10.1002/prot.22527  0.815
2009 Grosdidier S, Totrov M, Fernández-Recio J. Computer applications for prediction of protein-protein interactions and rational drug design. Advances and Applications in Bioinformatics and Chemistry : Aabc. 2: 101-23. PMID 21918619  0.85
2009 Mosca R, Pons C, Fernández-Recio J, Aloy P. Pushing structural information into the yeast interactome by high-throughput protein docking experiments. Plos Computational Biology. 5: e1000490. PMID 19714207 DOI: 10.1371/Journal.Pcbi.1000490  0.797
2009 Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P. FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics (Oxford, England). 25: 2544-51. PMID 19620099 DOI: 10.1093/Bioinformatics/Btp447  0.82
2009 Arafat Y, Kamruzzaman J, Karmakar GC, Fernandez-Recio J. Predicting protein-protein interfaces as clusters of optimal docking area points. International Journal of Data Mining and Bioinformatics. 3: 55-67. PMID 19432376 DOI: 10.1504/ijdmb.2009.023884  0.45
2009 Casasoli M, Federici L, Spinelli F, Di Matteo A, Vella N, Scaloni F, Fernandez-Recio J, Cervone F, De Lorenzo G. Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein. Proceedings of the National Academy of Sciences of the United States of America. 106: 7666-71. PMID 19372373 DOI: 10.1073/pnas.0812625106  0.467
2009 Bernadó P, Pérez Y, Blobel J, Fernández-Recio J, Svergun DI, Pons M. Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering. Protein Science : a Publication of the Protein Society. 18: 716-26. PMID 19309697 DOI: 10.1002/Pro.83  0.408
2009 Fernández-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Science. 11: 280-291. PMID 11790838 DOI: 10.1110/Ps.19202  0.677
2008 Grosdidier S, Fernández-Recio J. Identification of hot-spot residues in protein-protein interactions by computational docking. Bmc Bioinformatics. 9: 447. PMID 18939967 DOI: 10.1186/1471-2105-9-447  0.864
2008 Cheng TM, Blundell TL, Fernandez-Recio J. Structural assembly of two-domain proteins by rigid-body docking. Bmc Bioinformatics. 9: 441. PMID 18925951 DOI: 10.1186/1471-2105-9-441  0.553
2008 Hart SE, Howe CJ, Mizuguchi K, Fernandez-Recio J. Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum. Protein Engineering, Design & Selection : Peds. 21: 689-98. PMID 18824464 DOI: 10.1093/protein/gzn051  0.393
2008 Pallarès I, Fernández D, Comellas-Bigler M, Fernández-Recio J, Ventura S, Avilés FX, Bode W, Vendrell J. Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid). Acta Crystallographica. Section D, Biological Crystallography. 784-91. PMID 18566513 DOI: 10.1107/S0907444908013474  0.373
2008 Fernández-Recio J, Verma C. Theory and simulation. Editorial overview. Current Opinion in Structural Biology. 18: 131-3. PMID 18406601 DOI: 10.1016/J.Sbi.2008.03.001  0.181
2008 Bavro VN, Pietras Z, Furnham N, Pérez-Cano L, Fernández-Recio J, Pei XY, Misra R, Luisi B. Assembly and channel opening in a bacterial drug efflux machine. Molecular Cell. 30: 114-21. PMID 18406332 DOI: 10.1016/J.Molcel.2008.02.015  0.746
2008 Degryse B, Fernandez-Recio J, Citro V, Blasi F, Cubellis MV. In silico docking of urokinase plasminogen activator and integrins. Bmc Bioinformatics. S8. PMID 18387210 DOI: 10.1186/1471-2105-9-S2-S8  0.287
2008 Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J. Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins. 72: 848-62. PMID 18260112 DOI: 10.1002/Prot.21979  0.837
2008 Grosdidier S, Pons C, Solernou A, Fernández-Recio J. Prediction and scoring of docking poses with pyDock. Proteins. 69: 852-8. PMID 17876821 DOI: 10.1002/prot.21796  0.806
2008 Bonivento D, Pontiggia D, Matteo AD, Fernandez-Recio J, Salvi G, Tsernoglou D, Cervone F, Lorenzo GD, Federici L. Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins. Proteins. 70: 294-9. PMID 17876815 DOI: 10.1002/prot.21610  0.426
2007 Fort J, de la Ballina LR, Burghardt HE, Ferrer-Costa C, Turnay J, Ferrer-Orta C, Usón I, Zorzano A, Fernández-Recio J, Orozco M, Lizarbe MA, Fita I, Palacín M. The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. The Journal of Biological Chemistry. 282: 31444-52. PMID 17724034 DOI: 10.1074/jbc.M704524200  0.544
2007 Cheng TMK, Blundell TL, Fernandez-Recio J. PyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking Proteins: Structure, Function and Genetics. 68: 503-515. PMID 17444519 DOI: 10.1002/prot.21419  0.637
2007 Fernández D, Vendrell J, Avilés FX, Fernández-Recio J. Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis. Proteins. 68: 131-44. PMID 17407161 DOI: 10.1002/prot.21390  0.496
2007 Chandran V, Poljak L, Vanzo NF, Leroy A, Miguel RN, Fernandez-Recio J, Parkinson J, Burns C, Carpousis AJ, Luisi BF. Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. Journal of Molecular Biology. 367: 113-32. PMID 17234211 DOI: 10.1016/j.jmb.2006.12.014  0.313
2006 Bolanos-Garcia VM, Fernandez-Recio J, Allende JE, Blundell TL. Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit. Trends in Biochemical Sciences. 31: 654-61. PMID 17084631 DOI: 10.1016/J.Tibs.2006.10.005  0.757
2006 Casal E, Federici L, Zhang W, Fernandez-Recio J, Priego EM, Miguel RN, DuHadaway JB, Prendergast GC, Luisi BF, Laue ED. The crystal structure of the BAR domain from human Bin1/amphiphysin II and its implications for molecular recognition. Biochemistry. 45: 12917-28. PMID 17059209 DOI: 10.1021/Bi060717K  0.41
2006 Blundell TL, Fernández-Recio J. Cell biology: Brief encounters bolster contacts Nature. 444: 279-280. PMID 17051147 DOI: 10.1038/nature05306  0.419
2006 Yraola F, García-Vicente S, Fernandez-Recio J, Albericio F, Zorzano A, Marti L, Royo M. New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: analysis by SARs and computational docking. Journal of Medicinal Chemistry. 49: 6197-208. PMID 17034126 DOI: 10.1021/Jm051076E  0.368
2006 Chelliah V, Blundell TL, Fernández-Recio J. 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: 1669-1682. PMID 16488431 DOI: 10.1016/j.jmb.2006.01.001  0.653
2006 Federici L, Di Matteo A, Fernandez-Recio J, Tsernoglou D, Cervone F. Polygalacturonase inhibiting proteins: players in plant innate immunity? Trends in Plant Science. 11: 65-70. PMID 16406303 DOI: 10.1016/j.tplants.2005.12.005  0.409
2005 Sicilia F, Fernandez-Recio J, Caprari C, De Lorenzo G, Tsernoglou D, Cervone F, Federici L. The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea. Plant Physiology. 139: 1380-8. PMID 16244152 DOI: 10.1104/pp.105.067546  0.357
2005 Fernández-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions: Optimized desolvation for rigid-body docking Proteins. 60: 308-313. PMID 15981266 DOI: 10.1002/Prot.20575  0.63
2005 Federici L, Du D, Walas F, Matsumura H, Fernandez-Recio J, McKeegan KS, Borges-Walmsley MI, Luisi BF, Walmsley AR. The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 A resolution. The Journal of Biological Chemistry. 280: 15307-14. PMID 15684414 DOI: 10.1074/Jbc.M500401200  0.368
2004 Fernandez-Recio J, Walas F, Federici L, Pratap JV, Bavro VN, Miguel RN, Mizuguchi K, Luisi B. A model of a transmembrane drug-efflux pump from Gram-negative bacteria. Febs Letters. 578: 5-9. PMID 15581607 DOI: 10.1016/J.Febslet.2004.10.097  0.364
2004 Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 58: 134-143. PMID 15495260 DOI: 10.1002/Prot.20285  0.672
2004 López-Llano J, Maldonado S, Jain S, Lostao A, Godoy-Ruiz R, Sanchez-Ruiz JM, Cortijo M, Fernández-Recio J, Sancho J. The long and short flavodoxins: II. The role of the differentiating loop in apoflavodoxin stability and folding mechanism. The Journal of Biological Chemistry. 279: 47184-91. PMID 15317817 DOI: 10.1074/Jbc.M405791200  0.689
2004 Harmer NJ, Pellegrini L, Chirgadze D, Fernandez-Recio J, Blundell TL. 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: 629-640. PMID 14730967 DOI: 10.1021/bi035320k  0.774
2004 Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. Journal of Molecular Biology. 335: 843-865. PMID 14687579 DOI: 10.1016/J.Jmb.2003.10.069  0.682
2003 Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins. 52: 113-117. PMID 12784376 DOI: 10.1002/Prot.10383  0.567
2002 Sancho J, Bueno M, Campos LA, Fernández-Recio J, López J, Machicado C, Pedroso I, Toja M. The 'relevant' stability of proteins with equilibrium intermediates. The Scientific World Journal. 2: 1209-1215. PMID 12805903 DOI: 10.1100/Tsw.2002.196  0.763
2002 Fernandez-Recio J, Totrov M, Abagyan R. Screened charge electrostatic model in protein-protein docking simulations. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 552-63. PMID 11928507  0.579
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