Publications
2019
pyDockEneRes: per-residue decomposition of protein–protein docking energyMiguel Romero-Durana, Brian Jiménez-García, Juan Fernández-Recio.
Bioinformatics doi: 10.1093/bioinformatics/btz884 PubMed: 31808797
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 doi: 10.1371/journal.pone.0183643 PubMed: 28841721
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 doi: 10.1002/prot.25184 PubMed: 27701776
2016
Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters.Pallara, C., Rueda, M., Abagyan, R., Fernández-Recio, J. .
Journal of Chemical Theory and Computation doi: 10.1021/acs.jctc.6b00204 PubMed: 27294484
2015
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.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..
Journal of molecular biology doi: 10.1016/j.jmb.2015.07.016 PubMed: 26231283
pyDockSAXS: protein-protein complex structure by SAXS and computational docking.
Jiménez-García,B., Pons,C., Svergun,DI., Bernadó,P., Fernández-Recio,J..
Nucleic acids research doi: 10.1093/nar/gkv368 PubMed: 25897115
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,MP., Maskos,U., Setterblad,N., Janin,A., Calvo,F., Lebbé,C., Menashi,S., Fernandez-Recio,J., Mourah,S..
Oncotarget PubMed: 25825981
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,BO., Dahlbäck,B..
Thrombosis and haemostasis doi: 10.1160/TH14-09-0803 PubMed: 25716664
Inferring the microscopic surface energy of protein-protein interfaces from mutation data.
Moal,IH., Dapkūnas,J., Fernández-Recio,J..
Proteins doi: 10.1002/prot.24761 PubMed: 25586563
2014
Comment on 'protein-protein binding affinity prediction from amino acid sequence'.Moal,IH., Fernández-Recio,J..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu682 PubMed: 25381451
CCharPPI web server: computational characterization of protein-protein interactions from structure.
Moal,IH., Jiménez-García,B., Fernández-Recio,J..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu594 PubMed: 25183488
Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.
Lucas,M., Gaspar,AH., Pallara,C., Rojas,AL., Fernández-Recio,J., Machner,MP., Hierro,A..
Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.1405391111 PubMed: 25114243
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,RT., Barrio,R., Carracedo,A., Fernandez-Recio,J., Rodríguez,MS., Aillet,F..
Molecular oncology doi: 10.1016/j.molonc.2014.04.002 PubMed: 24816189
Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc.
Rosell,A., Meury,M., Álvarez-Marimon,E., Costa,M., Pérez-Cano,L., Zorzano,A., Fernández-Recio,J., Palacín,M., Fotiadis,D..
Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.1323779111 PubMed: 24516142
2013
Blind prediction of interfacial water positions in CAPRI.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., Fernández-Recio,J., Xu,J., Muthu,P., Praneeth Kilambi,K., Gray,JJ., Grudinin,S., Derevyanko,G., Mitchell,JC., Wieting,J., Kanamori,E., Tsuchiya,Y., Murakami,Y., Sarmiento,J., Standley,DM., Shirota,M., Kinoshita,K., Nakamura,H., Chavent,M., Ritchie,DW., Park,H., Ko,J., Lee,H., Seok,C., Shen,Y., Kozakov,D., Vajda,S., Kundrotas,PJ., Vakser,IA., Pierce,BG., Hwang,H., Vreven,T., Weng,Z., Buch,I., Farkash,E., Wolfson,HJ., Zacharias,M., Qin,S., Zhou,HX., Huang,SY., Zou,X., Wojdyla,JA., Kleanthous,C., Wodak,SJ..
Proteins doi: 10.1002/prot.24439 PubMed: 24155158
The scoring of poses in protein-protein docking: current capabilities and future directions.
Moal,IH., Torchala,M., Bates,PA., Fernández-Recio,J..
BMC bioinformatics doi: 10.1186/1471-2105-14-286 PubMed: 24079540
Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.
Agius,R., Torchala,M., Moal,IH., Fernández-Recio,J., Bates,PA..
PLoS computational biology doi: 10.1371/journal.pcbi.1003216 PubMed: 24039569
Conformational transitions in human translin enable nucleic acid binding.
Pérez-Cano,L., Eliahoo,E., Lasker,K., Wolfson,HJ., Glaser,F., Manor,H., Bernadó,P., Fernández-Recio,J..
Nucleic acids research doi: 10.1093/nar/gkt765 PubMed: 23980029
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,IH., Fernandez-Recio,J..
Proteins doi: 10.1002/prot.24387 PubMed: 23934865
Scoring functions for protein-protein interactions.
Moal,IH., Moretti,R., Baker,D., Fernández-Recio,J..
Current opinion in structural biology doi: 10.1016/j.sbi.2013.06.017 PubMed: 23871100
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
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., Perez-Cano,L., Pallara,C., Jimenez,B., Fernandez-Recio,J., Flores,S., Pacella,M., Praneeth Kilambi,K., Gray,JJ., Popov,P., Grudinin,S., Esquivel-Rodríguez,J., Kihara,D., Zhao,N., Korkin,D., Zhu,X., Demerdash,ON., Mitchell,JC., Kanamori,E., Tsuchiya,Y., Nakamura,H., Lee,H., Park,H., Seok,C., Sarmiento,J., Liang,S., Teraguchi,S., Standley,DM., Shimoyama,H., Terashi,G., Takeda-Shitaka,M., Iwadate,M., Umeyama,H., Beglov,D., Hall,DR., Kozakov,D., Vajda,S., Pierce,BG., Hwang,H., Vreven,T., Weng,Z., Huang,Y., Li,H., Yang,X., Ji,X., Liu,S., Xiao,Y., Zacharias,M., Qin,S., Zhou,HX., Huang,SY., Zou,X., Velankar,S., Janin,J., Wodak,SJ., Baker,D..
Proteins doi: 10.1002/prot.24356 PubMed: 23843247
Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD.
Chen,Y., Tascón,I., Neunuebel,MR., Pallara,C., Brady,J., Kinch,LN., Fernández-Recio,J., Rojas,AL., Machner,MP., Hierro,A..
PLoS pathogens doi: 10.1371/journal.ppat.1003382 PubMed: 23696742
pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.
Jiménez-García,B., Pons,C., Fernández-Recio,J..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btt262 PubMed: 23661696
SwarmDock: a server for flexible protein-protein docking.
Torchala,M., Moal,IH., Chaleil,RA., Fernandez-Recio,J., Bates,PA..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btt038 PubMed: 23343604
2012
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.Moal,IH., Fernández-Recio,J..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/bts489 PubMed: 22859501
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..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/bts454 PubMed: 22815362
Allosteric conversation in the androgen receptor ligand-binding domain surfaces.
Grosdidier,S., Carbó,LR., Buzón,V., Brooke,G., Nguyen,P., Baxter,JD., Bevan,C., Webb,P., Estébanez-Perpiñá,E., Fernández-Recio,J..
Molecular endocrinology (Baltimore, Md.) doi: 10.1210/me.2011-1281 PubMed: 22653923
Protein-protein docking and hot-spot prediction for drug discovery.
Grosdidier,S., Fernández-Recio,J..
Current pharmaceutical design PubMed: 22650255
A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data.
Pérez-Cano,L., Jiménez-García,B., Fernández-Recio,J..
Proteins doi: 10.1002/prot.24075 PubMed: 22488990
Theory and simulation: complexity and emergence.
Fernandez-Recio,J., Verma,C..
Current opinion in structural biology doi: 10.1016/j.sbi.2012.02.002 PubMed: 22417973
Established and emerging trends in computational drug discovery in the structural genomics era.
Taboureau,O., Baell,JB., Fernández-Recio,J., Villoutreix,BO..
Chemistry & biology doi: 10.1016/j.chembiol.2011.12.007 PubMed: 22284352
2011
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.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., Ko,JS., Lee,H., Seok,C., Bourquard,T., Bernauer,J., Poupon,A., Azé,J., Soner,S., Ovali,SK., Ozbek,P., Tal,NB., Haliloglu,T., Hwang,H., Vreven,T., Pierce,BG., Weng,Z., Pérez-Cano,L., Pons,C., Fernández-Recio,J., Jiang,F., Yang,F., Gong,X., Cao,L., Xu,X., Liu,B., Wang,P., Li,C., Wang,C., Robert,CH., Guharoy,M., Liu,S., Huang,Y., Li,L., Guo,D., Chen,Y., Xiao,Y., London,N., Itzhaki,Z., Schueler-Furman,O., Inbar,Y., Potapov,V., Cohen,M., Schreiber,G., Tsuchiya,Y., Kanamori,E., Standley,DM., Nakamura,H., Kinoshita,K., Driggers,CM., Hall,RG., Morgan,JL., Hsu,VL., Zhan,J., Yang,Y., Zhou,Y., Kastritis,PL., Bonvin,AM., Zhang,W., Camacho,CJ., Kilambi,KP., Sircar,A., Gray,JJ., Ohue,M., Uchikoga,N., Matsuzaki,Y., Ishida,T., Akiyama,Y., Khashan,R., Bush,S., Fouches,D., Tropsha,A., Esquivel-Rodríguez,J., Kihara,D., Stranges,PB., Jacak,R., Kuhlman,B., Huang,SY., Zou,X., Wodak,SJ., Janin,J., Baker,D..
Journal of molecular biology doi: 10.1016/j.jmb.2011.09.031 PubMed: 22001016
Prediction of protein-binding areas by small-world residue networks and application to docking.
Pons,C., Glaser,F., Fernandez-Recio,J..
BMC bioinformatics doi: 10.1186/1471-2105-12-378 PubMed: 21943333
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 doi: 10.1371/journal.pone.0021614 PubMed: 21789174
pyDockCG: new coarse-grained potential for protein-protein docking.
Solernou,A., Fernandez-Recio,J..
The journal of physical chemistry. B doi: 10.1021/jp112292b PubMed: 21506617
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., Fernandez-Recio,J..
Journal of chemical information and modeling doi: 10.1021/ci100353e PubMed: 21214199
2010
Dissection and prediction of RNA-binding sites on proteins.Pérez-Cano,L., Fernández-Recio,J..
Biomolecular concepts doi: 10.1515/bmc.2010.037 PubMed: 25962008
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.
Pons,C., D'Abramo,M., Svergun,DI., Orozco,M., Bernadó,P., Fernández-Recio,J..
Journal of molecular biology doi: 10.1016/j.jmb.2010.08.029 PubMed: 20804770
Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.
Pons,C., Solernou,A., Perez-Cano,L., Grosdidier,S., Fernandez-Recio,J..
Proteins doi: 10.1002/prot.22773 PubMed: 20602351
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation.
Solernou,A., Fernandez-Recio,J..
BMC bioinformatics doi: 10.1186/1471-2105-11-352 PubMed: 20584304
Theory and simulation: integrating models into experimental scenarios.
Fernández-Recio,J., Verma,C..
Current opinion in structural biology doi: 10.1016/j.sbi.2010.02.002 PubMed: 20226653
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..
Organic & biomolecular chemistry doi: 10.1039/b919671d PubMed: 20135035
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 research doi: 10.1093/nar/gkp1230 PubMed: 20081200
2009
Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials.Pérez-Cano,L., Solernou,A., Pons,C., Fernández-Recio,J..
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing PubMed: 19908381
Present and future challenges and limitations in protein-protein docking.
Pons,C., Grosdidier,S., Solernou,A., Pérez-Cano,L., Fernández-Recio,J..
Proteins doi: 10.1002/prot.22564 PubMed: 19731373
Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins.
Pérez-Cano,L., Fernández-Recio,J..
Proteins doi: 10.1002/prot.22527 PubMed: 19714772
Pushing structural information into the yeast interactome by high-throughput protein docking experiments.
Mosca,R., Pons,C., Fernández-Recio,J., Aloy,P..
PLoS computational biology doi: 10.1371/journal.pcbi.1000490 PubMed: 19714207
FRODOCK: a new approach for fast rotational protein-protein docking.
Garzon,JI., Lopéz-Blanco,JR., Pons,C., Kovacs,J., Abagyan,R., Fernandez-Recio,J., Chacon,P..
Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btp447 PubMed: 19620099
Docking and scoring: applications to drug discovery in the interactomics era.
Grosdidier,S., Fernández-Recio,J..
Expert opinion on drug discovery doi: 10.1517/17460440903002067 PubMed: 23489159
Predicting protein-protein interfaces as clusters of optimal docking area points.
Arafat,Y., Kamruzzaman,J., Karmakar,GC., Fernandez-Recio,J..
International journal of data mining and bioinformatics PubMed: 19432376
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., Fernandez-Recio,J., Cervone,F., De Lorenzo,G..
Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.0812625106 PubMed: 19372373
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,DI., Pons,M..
Protein science : a publication of the Protein Society doi: 10.1002/pro.83 PubMed: 19309697
Computer applications for prediction of protein-protein interactions and rational drug design.
Grosdidier,S., Totrov,M., Fernández-Recio,J..
Advances and applications in bioinformatics and chemistry : AABC PubMed: 21918619
2008
Identification of hot-spot residues in protein-protein interactions by computational docking.Grosdidier,S., Fernández-Recio,J..
BMC bioinformatics doi: 10.1186/1471-2105-9-447 PubMed: 18939967
Structural assembly of two-domain proteins by rigid-body docking.
Cheng,TM., Blundell,TL., Fernandez-Recio,J..
BMC bioinformatics doi: 10.1186/1471-2105-9-441 PubMed: 18925951
Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum.
Hart,SE., Howe,CJ., Mizuguchi,K., Fernandez-Recio,J..
Protein engineering, design & selection : PEDS doi: 10.1093/protein/gzn051 PubMed: 18824464
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,FX., Bode,W., Vendrell,J..
Acta crystallographica. Section D, Biological crystallography doi: 10.1107/S0907444908013474 PubMed: 18566513
In silico docking of urokinase plasminogen activator and integrins.
Degryse,B., Fernandez-Recio,J., Citro,V., Blasi,F., Cubellis,MV..
BMC bioinformatics doi: 10.1186/1471-2105-9-S2-S8 PubMed: 18387210
Theory and simulation. Editorial overview.
Fernández-Recio,J., Verma,C..
Current opinion in structural biology doi: 10.1016/j.sbi.2008.03.001 PubMed: 18406601
Assembly and channel opening in a bacterial drug efflux machine.
Bavro,VN., Pietras,Z., Furnham,N., Pérez-Cano,L., Fernández-Recio,J., Pei,XY., Misra,R., Luisi,B..
Molecular cell doi: 10.1016/j.molcel.2008.02.015 PubMed: 18406332
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.
Medina,M., Abagyan,R., Gómez-Moreno,C., Fernandez-Recio,J..
Proteins doi: 10.1002/prot.21979 PubMed: 18260112
2007
Prediction and scoring of docking poses with pyDock.Grosdidier,S., Pons,C., Solernou,A., Fernández-Recio,J..
Proteins doi: 10.1002/prot.21796 PubMed: 17876821
Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.
Bonivento,D., Pontiggia,D., Matteo,AD., Fernandez-Recio,J., Salvi,G., Tsernoglou,D., Cervone,F., Lorenzo,GD., Federici,L..
Proteins doi: 10.1002/prot.21610 PubMed: 17876815
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.
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 Journal of biological chemistry doi: 10.1074/jbc.M704524200 PubMed: 17724034
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.
Cheng,TM., Blundell,TL., Fernandez-Recio,J..
Proteins doi: 10.1002/prot.21419 PubMed: 17444519
Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis.
Fernández,D., Vendrell,J., Avilés,FX., Fernández-Recio,J..
Proteins doi: 10.1002/prot.21390 PubMed: 17407161
Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.
Chandran,V., Poljak,L., Vanzo,NF., Leroy,A., Miguel,RN., Fernandez-Recio,J., Parkinson,J., Burns,C., Carpousis,AJ., Luisi,BF..
Journal of molecular biology doi: 10.1016/j.jmb.2006.12.014 PubMed: 17234211
2006
Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit.Bolanos-Garcia,VM., Fernandez-Recio,J., Allende,JE., Blundell,TL..
Trends in biochemical sciences doi: 10.1016/j.tibs.2006.10.005 PubMed: 17084631
The crystal structure of the BAR domain from human Bin1/amphiphysin II and its implications for molecular recognition.
Casal,E., Federici,L., Zhang,W., Fernandez-Recio,J., Priego,EM., Miguel,RN., DuHadaway,JB., Prendergast,GC., Luisi,BF., Laue,ED..
Biochemistry doi: 10.1021/bi060717k PubMed: 17059209
Cell biology: brief encounters bolster contacts.
Blundell,TL., Fernández-Recio,J..
Nature doi: 10.1038/nature05306 PubMed: 17051147
New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: analysis by SARs and computational docking.
Yraola,F., García-Vicente,S., Fernandez-Recio,J., Albericio,F., Zorzano,A., Marti,L., Royo,M..
Journal of medicinal chemistry doi: 10.1021/jm051076e PubMed: 17034126
Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment.
Chelliah,V., Blundell,TL., Fernández-Recio,J..
Journal of molecular biology doi: 10.1016/j.jmb.2006.01.001 PubMed: 16488431
Polygalacturonase inhibiting proteins: players in plant innate immunity?
Federici,L., Di Matteo,A., Fernandez-Recio,J., Tsernoglou,D., Cervone,F..
Trends in plant science doi: 10.1016/j.tplants.2005.12.005 PubMed: 16406303
2005
Data mining of molecular dynamics trajectories of nucleic acids.Noy,A., Meyer,T., Rueda,M., Ferrer,C., Valencia,A., Pérez,A., de la Cruz,X., López-Bes,JM., Pouplana,R., Fernandez-Recio,J., Luque,FJ., Orozco,M..
Journal of biomolecular structure & dynamics doi: 10.1080/07391102.2006.10507070 PubMed: 16363879
The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea.
Sicilia,F., Fernandez-Recio,J., Caprari,C., De Lorenzo,G., Tsernoglou,D., Cervone,F., Federici,L..
Plant physiology doi: 10.1104/pp.105.067546 PubMed: 16244152
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
Fernández-Recio,J., Abagyan,R., Totrov,M..
Proteins doi: 10.1002/prot.20575 PubMed: 15981266
The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 A resolution.
Federici,L., Du,D., Walas,F., Matsumura,H., Fernandez-Recio,J., McKeegan,KS., Borges-Walmsley,MI., Luisi,BF., Walmsley,AR..
The Journal of biological chemistry doi: 10.1074/jbc.M500401200 PubMed: 15684414
2004
A model of a transmembrane drug-efflux pump from Gram-negative bacteria.Fernandez-Recio,J., Walas,F., Federici,L., Venkatesh Pratap,J., Bavro,VN., Miguel,RN., Mizuguchi,K., Luisi,B..
FEBS letters doi: 10.1016/j.febslet.2004.10.097 PubMed: 15581607
Optimal docking area: a new method for predicting protein-protein interaction sites.
Fernandez-Recio,J., Totrov,M., Skorodumov,C., Abagyan,R..
Proteins doi: 10.1002/prot.20285 PubMed: 15495260
The long and short flavodoxins: II. The 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,JM., Cortijo,M., Fernández-Recio,J., Sancho,J..
The Journal of biological chemistry doi: 10.1074/jbc.M405791200 PubMed: 15317817
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,NJ., Pellegrini,L., Chirgadze,D., Fernandez-Recio,J., Blundell,TL..
Biochemistry doi: 10.1021/bi035320k PubMed: 14730967
2003
Identification of protein-protein interaction sites from docking energy landscapes.Fernández-Recio,J., Totrov,M., Abagyan,R..
Journal of molecular biology PubMed: 14687579
The 'relevant' stability of proteins with equilibrium intermediates.
Sancho,J., Bueno,M., Campos,LA., Fernández-Recio,J., Irún,MP., López,J., Machicado,C., Pedroso,I., Toja,M..
TheScientificWorldJournal doi: 10.1100/tsw.2002.196 PubMed: 12805903
ICM-DISCO docking by global energy optimization with fully flexible side-chains.
Fernández-Recio,J., Totrov,M., Abagyan,R..
Proteins doi: 10.1002/prot.10383 PubMed: 12784376
2002
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