Publications

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

Screened charge electrostatic model in protein-protein docking simulations.
Fernandez-Recio,J., Totrov,M., Abagyan,R..
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  PubMed: 11928507

Soft protein-protein docking in internal coordinates.
Fernández-Recio,J., Totrov,M., Abagyan,R..
Protein science : a publication of the Protein Society  PubMed: 11790838

2001

Apoflavodoxin folding mechanism: an alpha/beta protein with an essentially off-pathway intermediate.
Fernández-Recio,J., Genzor,CG., Sancho,J..
Biochemistry  PubMed: 11735406

1999

Energetics of a hydrogen bond (charged and neutral) and of a cation-pi interaction in apoflavodoxin.
Fernández-Recio,J., Romero,A., Sancho,J..
Journal of molecular biology  doi: 10.1006/jmbi.1999.2863  PubMed: 10388575

Apoflavodoxin: structure, stability, and FMN binding.
Maldonado,S., Lostao,A., Irún,MP., Férnandez-Recio,J., Gustavo Genzor,C., Begoña González,E., Rubio,JA., Luquita,A., Daoudi,F., Sancho,J..
Biochimie  PubMed: 9893940

1998

Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency.
Fernández-Recio,J., Sancho,J..
FEBS letters  PubMed: 9657391

1997

The tryptophan/histidine interaction in alpha-helices.
Fernández-Recio,J., Vázquez,A., Civera,C., Sevilla,P., Sancho,J..
Journal of molecular biology  doi: 10.1006/jmbi.1996.0831  PubMed: 9096217