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Juan Fernandez-Recio

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Physiology

Protein Folding

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Amino Acid Sequences

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Publications

TOP 3
Mieczyslaw Torchala; Raphael A G Chaleil; Juan Fernandez-Recio; Iain H Moal; Paul A Bates
SwarmDock: a server for flexible protein-protein docking.
Iain H Moal; Juan Fernandez-Recio
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.
Carles Pons; Harald Servat; Xavier Aguilar; Daniel Cabrera-Benítez; Cecilia González-Álvarez; Daniel Jiménez-González; Juan Fernandez-Recio
Cell-Dock: high-performance protein-protein docking.

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All Publications

2013: Mieczyslaw Torchala; Raphael A G Chaleil; Juan Fernandez-Recio; Iain H Moal; Paul A Bates
SwarmDock: a server for flexible protein-protein docking.
Bioinformatics (Oxford, England) 2013;29(6):807-9.
2012: Iain H Moal; Juan Fernandez-Recio
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.
Bioinformatics (Oxford, England) 2012;28(20):2600-7.
2012: Carles Pons; Harald Servat; Xavier Aguilar; Daniel Cabrera-Benítez; Cecilia González-Álvarez; Daniel Jiménez-González; Juan Fernandez-Recio
Cell-Dock: high-performance protein-protein docking.
Bioinformatics (Oxford, England) 2012;28(18):2394-6.
2012: Solène Grosdidier; Phuong Nguyen; Paul Webb; John D Baxter; Charlotte Bevan; Greg Brooke; Víctor Buzón; Laia R Carbó; Eva Estébanez-Perpiñá; Juan Fernandez-Recio
Allosteric conversation in the androgen receptor ligand-binding domain surfaces.
Molecular endocrinology (Baltimore, Md.) 2012;26(7):1078-90.
2012: Laura Pérez-Cano; Brian Jiménez-García; Juan Fernandez-Recio
A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data.
Proteins 2012;80(7):1872-82.
2012: Juan Fernandez-Recio; Chandra Verma
Theory and simulation: complexity and emergence.
Current opinion in structural biology 2012;22(2):127-9.
2012: Olivier Taboureau; Jonathan B Baell; Juan Fernandez-Recio; Bruno O Villoutreix
Established and emerging trends in computational drug discovery in the structural genomics era.
Chemistry & biology 2012;19(1):29-41.
2012: Solene Grosdidier; Juan Fernandez-Recio
Protein-protein docking and hot-spot prediction for drug discovery.
Current pharmaceutical design 2012;18(30):4607-18.
2011: Albert Solernou; Juan Fernandez-Recio
pyDockCG: new coarse-grained potential for protein-protein docking.
The journal of physical chemistry. B 2011;115(19):6032-9.
2011: Carles Pons; David Talavera; Xavier de la Cruz; Modesto Orozco; Juan Fernandez-Recio
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking.
Journal of chemical information and modeling 2011;51(2):370-7.
2011: Carles Pons; Fabian Glaser; Juan Fernandez-Recio
Prediction of protein-binding areas by small-world residue networks and application to docking.
BMC bioinformatics 2011;12():378.
2011: Laura Helft; Teresa Koller; Vignyan Reddy; Xiyang Chen; Luca Federici; Juan Fernandez-Recio; Rishabh Gupta; Andrew Bent
LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.
PloS one 2011;6(7):e21614.
2010: Carles Pons; Albert Solernou; Laura Perez-Cano; Solène Grosdidier; Juan Fernandez-Recio
Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.
Proteins 2010;78(15):3182-8.
2010: Carles Pons; Marco D'Abramo; Dmitri I Svergun; Modesto Orozco; Pau Bernadó; Juan Fernandez-Recio
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.
Journal of molecular biology 2010;403(2):217-30.
2010: Elad Eliahoo; Ron Ben Yosef; Laura Pérez-Cano; Juan Fernandez-Recio; Fabian Glaser; Haim Manor
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 2010;38(9):2975-89.
2010: Juan Fernandez-Recio; Chandra Verma
Theory and simulation: integrating models into experimental scenarios.
Current opinion in structural biology 2010;20(2):139-41.
2010: Miriam Alías; Sara Ayuso-Tejedor; Juan Fernandez-Recio; Carlos Cativiela; javier sancho
Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine.
Organic & biomolecular chemistry 2010;8(4):788-92.
2010: Albert Solernou; Juan Fernandez-Recio
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation.
BMC bioinformatics 2010;11():352.
2010: Laura Pérez-Cano; Albert Solernou; Carles Pons; Juan Fernandez-Recio
Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2010;():293-301.
2010: Carles Pons; Solène Grosdidier; Albert Solernou; Laura Pérez-Cano; Juan Fernandez-Recio
Present and future challenges and limitations in protein-protein docking.
Proteins 2010;78(1):95-108.
2010: Laura Pérez-Cano; Juan Fernandez-Recio
Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins.
Proteins 2010;78(1):25-35.
2009: José Ignacio Garzon; José Ramón Lopéz-Blanco; Carles Pons; Julio Kovacs; Ruben Abagyan; Juan Fernandez-Recio; Pablo Chacon
FRODOCK: a new approach for fast rotational protein-protein docking.
Bioinformatics (Oxford, England) 2009;25(19):2544-51.
2009: Roberto Mosca; Carles Pons; Juan Fernandez-Recio; Patrick Aloy
Pushing structural information into the yeast interactome by high-throughput protein docking experiments.
PLoS computational biology 2009;5(8):e1000490.
2009: Solène Grosdidier; Juan Fernandez-Recio
Docking and scoring: applications to drug discovery in the interactomics era.
Expert opinion on drug discovery 2009;4(6):673-86.
2009: Manuela Casasoli; Luca Federici; Francesco Spinelli; Adele Di Matteo; Nicoletta Vella; Flavio Scaloni; Juan Fernandez-Recio; Felice Cervone; Giulia De Lorenzo
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 2009;106(18):7666-71.
2009: Pau Bernadó; Yolanda Pérez; Jascha Blobel; Juan Fernandez-Recio; Dmitri I Svergun; Miquel Pons
Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering.
Protein science : a publication of the Protein Society 2009;18(4):716-26.
2009: Solène Grosdidier; Max Totrov; Juan Fernandez-Recio
Computer applications for prediction of protein-protein interactions and rational drug design.
Advances and applications in bioinformatics and chemistry : AABC 2009;2():101-23.
2009: Yasir Arafat; Joarder Kamruzzaman; Gour C Karmakar; Juan Fernandez-Recio
Predicting protein-protein interfaces as clusters of optimal docking area points.
International journal of data mining and bioinformatics 2009;3(1):55-67.
2008: Sarah E Hart; Christopher J Howe; Kenji Mizuguchi; Juan Fernandez-Recio
Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum.
Protein engineering, design & selection : PEDS 2008;21(12):689-98.
2008: Milagros Medina; Ruben Abagyan; Carlos Gómez-Moreno; Juan Fernandez-Recio
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.
Proteins 2008;72(3):848-62.
2008: Irantzu Pallarès; Daniel Fernández; Mireia Comellas-Bigler; Juan Fernandez-Recio; Salvador Ventura; Francesc X Avilés; Wolfram Bode; Josep Vendrell
Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid).
Acta crystallographica. Section D, Biological crystallography 2008;D64(Pt 7):784-91.
2008: Vassiliy N Bavro; Zbigniew Pietras; Nicholas Furnham; Laura Pérez-Cano; Juan Fernandez-Recio; Xue Yuan Pei; Rajeev Misra; Ben F Luisi
Assembly and channel opening in a bacterial drug efflux machine.
Molecular cell 2008;30(1):114-21.
2008: Juan Fernandez-Recio; Chandra Verma
Theory and simulation. Editorial overview.
Current opinion in structural biology 2008;18(2):131-3.
2008: Solène Grosdidier; Juan Fernandez-Recio
Identification of hot-spot residues in protein-protein interactions by computational docking.
BMC bioinformatics 2008;9():447.
2008: Tammy M K Cheng; Tom L Blundell; Juan Fernandez-Recio
Structural assembly of two-domain proteins by rigid-body docking.
BMC bioinformatics 2008;9():441.
2008: Bernard Degryse; Juan Fernandez-Recio; Valentina Citro; Francescol Blasi; Maria Vittoria Cubellis
In silico docking of urokinase plasminogen activator and integrins.
BMC bioinformatics 2008;9 Suppl 2():S8.
2008: Daniele Bonivento; Daniela Pontiggia; Adele Di Matteo; Juan Fernandez-Recio; Gianni Salvi; Demetrius Tsernoglou; Felice Cervone; Giulia De Lorenzo; Luca Federici
Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.
Proteins 2008;70(1):294-9.
2007: Solène Grosdidier; Carles Pons; Albert Solernou; Juan Fernandez-Recio
Prediction and scoring of docking poses with pyDock.
Proteins 2007;69(4):852-8.
2007: Joana Fort; Laura R de la Ballina; Hans E Burghardt; Carles Ferrer-Costa; Javier Turnay; Cristina Ferrer-Orta; Isabel Usón; Antonio Zorzano; Juan Fernandez-Recio; Modesto Orozco; M Antonia Lizarbe; Ignacio Fita; Manuel Palacín
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.
The Journal of biological chemistry 2007;282(43):31444-52.
2007: Tammy Man-Kuang Cheng; Tom L Blundell; Juan Fernandez-Recio
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.
Proteins 2007;68(2):503-15.
2007: Daniel Fernández; Josep Vendrell; Francesc X Avilés; Juan Fernandez-Recio
Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis.
Proteins 2007;68(1):131-44.
2007: Vidya Chandran; Leonora Poljak; Nathalie F Vanzo; Anne Leroy; Ricardo Núñez Miguel; Juan Fernandez-Recio; James Parkinson; Christopher Burns; Agamemnon J Carpousis; Ben F Luisi
Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.
Journal of molecular biology 2007;367(1):113-32.
2006: Victor Martin Bolanos-Garcia; Juan Fernandez-Recio; Jorge E Allende; Tom L Blundell
Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit.
Trends in biochemical sciences 2006;31(12):654-61.
2006: Tom L Blundell; Juan Fernandez-Recio
Cell biology: brief encounters bolster contacts.
Nature 2006;444(7117):279-80.
2006: Eva Casal; Luca Federici; Wei Zhang; Juan Fernandez-Recio; Eva-Maria Priego; Ricardo Núñez Miguel; James B DuHadaway; George C Prendergast; Ben F Luisi; Ernest D Laue
The crystal structure of the BAR domain from human Bin1/amphiphysin II and its implications for molecular recognition.
Biochemistry 2006;45(43):12917-28.
2006: Francesc Yraola; Silvia García-Vicente; Juan Fernandez-Recio; Fernando Albericio; Antonio Zorzano; Luc Marti; Miriam Royo
New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: analysis by SARs and computational docking.
Journal of medicinal chemistry 2006;49(21):6197-208.
2006: Vijayalakshmi Chelliah; Tom L Blundell; Juan Fernandez-Recio
Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment.
Journal of molecular biology 2006;357(5):1669-82.
2006: Luca Federici; Adele Di Matteo; Juan Fernandez-Recio; Demetrius Tsernoglou; Felice Cervone
Polygalacturonase inhibiting proteins: players in plant innate immunity?
Trends in plant science 2006;11(2):65-70.
2006: Agnes Noy; Tim Meyer; Manuel Rueda; Carles Ferrer; Antonion Valencia; Alberto Pérez; Xavier de la Cruz; J M López-Bes; SOLE POUPLANA; Juan Fernandez-Recio; F Javier Luque; Modesto Orozco
Data mining of molecular dynamics trajectories of nucleic acids.
Journal of biomolecular structure & dynamics 2006;23(4):447-56.
2005: Francesca Sicilia; Juan Fernandez-Recio; Claudio Caprari; Giulia De Lorenzo; Demetrius Tsernoglou; Felice Cervone; Luca Federici
The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea.
Plant physiology 2005;139(3):1380-8.
2005: Juan Fernandez-Recio; Ruben Abagyan; Maxim Totrov
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
Proteins 2005;60(2):308-13.
2005: Luca Federici; Dijun Du; Fabien Walas; Hiroyoshi Matsumura; Juan Fernandez-Recio; Kenneth S McKeegan; M Ines Borges-Walmsley; Ben F Luisi; Adrian R Walmsley
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 2005;280(15):15307-14.
2005: Juan Fernandez-Recio; Maxim Totrov; Constantin Skorodumov; Ruben Abagyan
Optimal docking area: a new method for predicting protein-protein interaction sites.
Proteins 2005;58(1):134-43.
2004: Juan Fernandez-Recio; Fabien Walas; Luca Federici; J Venkatesh Pratap; Vassiliy N Bavro; Ricardo Núñez Miguel; Kenji Mizuguchi; Ben F Luisi
A model of a transmembrane drug-efflux pump from Gram-negative bacteria.
FEBS letters 2004;578(1-2):5-9.
2004: Jon López-Llano; Susana Maldonado; Shandya Jain; Anabel Lostao; Raquel Godoy-Ruiz; Jose M Sanchez-Ruiz; Manuel Cortijo; Juan Fernandez-Recio; javier sancho
The long and short flavodoxins: II. The role of the differentiating loop in apoflavodoxin stability and folding mechanism.
The Journal of biological chemistry 2004;279(45):47184-91.
2004: Nicholas J Harmer; Luca Pellegrini; Dimitri Y Chirgadze; Juan Fernandez-Recio; Tom L Blundell
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 2004;43(3):629-40.
2004: Juan Fernandez-Recio; Maxim Totrov; Ruben Abagyan
Identification of protein-protein interaction sites from docking energy landscapes.
Journal of molecular biology 2004;335(3):843-65.
2003: Juan Fernandez-Recio; Maxim Totrov; Ruben Abagyan
ICM-DISCO docking by global energy optimization with fully flexible side-chains.
Proteins 2003;52(1):113-7.
2002: javier sancho; Marta Bueno; Luis A Campos; Juan Fernandez-Recio; María Pilar Irún; Jon López; Claudia Machicado; Idolka Pedroso; Miguel Toja
The 'relevant' stability of proteins with equilibrium intermediates.
TheScientificWorldJournal 2002;2():1209-15.
2002: Juan Fernandez-Recio; Maxim Totrov; Ruben Abagyan
Soft protein-protein docking in internal coordinates.
Protein science : a publication of the Protein Society 2002;11(2):280-91.
2002: Juan Fernandez-Recio; Maxim Totrov; Ruben Abagyan
Screened charge electrostatic model in protein-protein docking simulations.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():552-63.
2001: Juan Fernandez-Recio; C G Genzor; javier sancho
Apoflavodoxin folding mechanism: an alpha/beta protein with an essentially off-pathway intermediate.
Biochemistry 2001;40(50):15234-45.
1999: Juan Fernandez-Recio; Antonio Romero; javier sancho
Energetics of a hydrogen bond (charged and neutral) and of a cation-pi interaction in apoflavodoxin.
Journal of molecular biology 1999;290(1):319-30.
1998: Juan Fernandez-Recio; javier sancho
Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency.
FEBS letters 1998;429(1):99-103.
1997: Juan Fernandez-Recio; A Vázquez; C Civera; P Sevilla; javier sancho
The tryptophan/histidine interaction in alpha-helices.
Journal of molecular biology 1997;267(1):184-97.