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1

Hot-spot analysis for drug discovery targeting protein-protein interactions

Rosell, Mireia, Fernández-Recio, Juan

Journal:

Expert Opinion on Drug Discovery

Year:

2018

Language:

english

File:

PDF, 1.72 MB

english, 2018

2

pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein–protein docking

Tammy Man-Kuang Cheng, Tom L. Blundell, Juan Fernandez-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 436 KB

english, 2007

3

Scoring functions for protein–protein interactions

Moal, Iain H, Moretti, Rocco, Baker, David, Fernández-Recio, Juan

Journal:

Current Opinion in Structural Biology

Year:

2013

Language:

english

File:

PDF, 833 KB

english, 2013

4

Lo que la memoria nos trae desde el recuerdo: Patrimonio cinematográfico, televisivo, radiofónico y publicitario

Marcos Recio, Juan Carlos, De la Cuadra de Colmenares, Elena, Fernández Sande, Manuel

Journal:

Revista General de Información y Documentación

Year:

2018

File:

PDF, 531 KB

2018

5

Investigation of the diaphorase reaction of ferredoxin-NADP+ reductase by electrochemical methods

Juan Madoz, Juan Fernández-Recio, Carlos Gómez-Moreno, Vı́ctor M. Fernández

Journal:

Bioelectrochemistry and Bioenergetics

Year:

1998

Language:

english

File:

PDF, 112 KB

english, 1998

6

Prediction of protein-binding areas by small-world residue networks and application to docking

Carles Pons, Fabian Glaser, Juan Fernandez-Recio

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 471 KB

english, 2011

7

Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering

Pau Bernadó, Yolanda Pérez, Jascha Blobel, Juan Fernández-Recio, Dmitri I. Svergun, Miquel Pons

Journal:

Protein Science

Year:

2009

Language:

english

File:

PDF, 490 KB

english, 2009

8

ICM-DISCO docking by global energy optimization with fully flexible side-chains

Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 445 KB

english, 2003

9

Optimal docking area: A new method for predicting protein–protein interaction sites

Juan Fernandez-Recio, Max Totrov, Constantin Skorodumov, Ruben Abagyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 296 KB

english, 2005

10

Improving CAPRI predictions: Optimized desolvation for rigid-body docking

Juan Fernández-Recio, Ruben Abagyan, Maxim Totrov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 214 KB

english, 2005

11

Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis

Daniel Fernández, Josep Vendrell, Francesc X. Avilés, Juan Fernández-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 708 KB

english, 2007

12

Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins

Daniele Bonivento, Daniela Pontiggia, Adele Di Matteo, Juan Fernandez-Recio, Gianni Salvi, Demetrius Tsernoglou, Felice Cervone, Giulia De Lorenzo, Luca Federici

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 243 KB

english, 2008

13

Prediction and scoring of docking poses with pyDock

Solène Grosdidier, Carles Pons, Albert Solernou, Juan Fernández-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 220 KB

english, 2007

14

Docking analysis of transient complexes: Interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin

Milagros Medina, Ruben Abagyan, Carlos Gómez-Moreno, Juan Fernandez-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.17 MB

english, 2008

15

Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins

Laura Pérez-Cano, Juan Fernández-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 442 KB

english, 2010

16

Present and future challenges and limitations in protein–protein docking

Carles Pons, Solène Grosdidier, Albert Solernou, Laura Pérez-Cano, Juan Fernández-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 364 KB

english, 2010

17

Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain–domain assembly and protein-RNA binding

Carles Pons, Albert Solernou, Laura Perez-Cano, Solène Grosdidier, Juan Fernandez-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 276 KB

english, 2010

18

The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona

Juan Fernández-Recio, Michael J. E. Sternberg

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 51 KB

english, 2010

19

H-bond network optimization in protein–protein complexes: Are all-atom force field scores enough?

Diego Masone, Israel Cabeza de Vaca, Carles Pons, Juan Fernandez Recio, Victor Guallar

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 2.28 MB

english, 2012

20

Cell biology: Brief encounters bolster contacts

Blundell, Tom L., Fernández-Recio, Juan

Journal:

Year:

2006

Language:

english

File:

PDF, 449 KB

english, 2006

21

Soft protein–protein docking in internal coordinates

Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 999 KB

english, 2002

22

A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data

Laura Pérez-Cano, Brian Jiménez-García, Juan Fernández-Recio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 937 KB

english, 2012

23

Prediction of protein binding sites and hot spots

Juan Fernández-Recio

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 576 KB

english, 2011

24

Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era

Olivier Taboureau, Jonathan B. Baell, Juan Fernández-Recio, Bruno O. Villoutreix

Journal:

Chemistry & Biology

Year:

2012

Language:

english

File:

PDF, 786 KB

english, 2012

25

Editorial

Juan Fernández-Recio, Chandra Verma

Journal:

Current Opinion in Structural Biology

Year:

2008

Language:

english

File:

PDF, 103 KB

english, 2008

26

Theory and simulation: integrating models into experimental scenarios

Juan Fernández-Recio, Chandra Verma

Journal:

Current Opinion in Structural Biology

Year:

2010

Language:

english

File:

PDF, 85 KB

english, 2010

27

Theory and simulation: complexity and emergence

Juan Fernandez-Recio, Chandra Verma

Journal:

Current Opinion in Structural Biology

Year:

2012

Language:

english

File:

PDF, 165 KB

english, 2012

28

Identifying interaction motifs in CK2β – a ubiquitous kinase regulatory subunit

Victor Martin Bolanos-Garcia, Juan Fernandez-Recio, Jorge E. Allende, Tom L. Blundell

Journal:

Trends in Biochemical Sciences

Year:

2006

Language:

english

File:

PDF, 1.30 MB

english, 2006

29

Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation

Albert Solernou, Juan Fernandez-Recio

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.91 MB

english, 2010

30

Structural assembly of two-domain proteins by rigid-body docking

Tammy MK Cheng, Tom L Blundell, Juan Fernandez-Recio

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.55 MB

english, 2008

31

Identification of hot-spot residues in protein-protein interactions by computational docking

Solène Grosdidier, Juan Fernández-Recio

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 994 KB

english, 2008

32

In silico docking of urokinase plasminogen activator and integrins

Bernard Degryse, Juan Fernandez-Recio, Valentina Citro, Francescol Blasi, Maria Vittoria Cubellis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.88 MB

english, 2008

33

The Tryptophan/Histidine interaction in α-helices

Juan Fernández-Recio, Ana Vázquez, Concepción Civera, Paz Sevilla, Javier Sancho

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 442 KB

english, 1997

34

The tryptophan/histidine interaction in α-helices

Juan Fernández-Recio, Ana Vázquez, Concepción Civera, Paz Sevilla, Javier Sancho

Journal:

Journal of Molecular Biology

Year:

1997

File:

PDF, 76 KB

1997

35

Energetics of a hydrogen bond (charged and neutral) and of a cation-π interaction in apoflavodoxin

Juan Fernández-Recio, Antonio Romero, Javier Sancho

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 321 KB

english, 1999

36

A model of a transmembrane drug-efflux pump from Gram-negative bacteria

Juan Fernandez-Recio, Fabien Walas, Luca Federici, J. Venkatesh Pratap, Vassiliy N. Bavro, Ricardo Nunez Miguel, Kenji Mizuguchi, Ben Luisi

Journal:

Year:

2004

Language:

english

File:

PDF, 695 KB

english, 2004

37

Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes

Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 6.46 MB

english, 2004

38

Efficient Restraints for Protein–Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment

Vijayalakshmi Chelliah, Tom L. Blundell, Juan Fernández-Recio

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 851 KB

english, 2006

39

Recognition and Cooperation Between the ATP-dependent RNA Helicase RhlB and Ribonuclease RNase E

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

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 3.50 MB

english, 2007

40

Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

Carles Pons, Marco D’Abramo, Dmitri I. Svergun, Modesto Orozco, Pau Bernadó, Juan Fernández-Recio

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 790 KB

english, 2010

41

Assembly and Channel Opening in a Bacterial Drug Efflux Machine

Vassiliy N. Bavro, Zbigniew Pietras, Nicholas Furnham, Laura Pérez-Cano, Juan Fernández-Recio, Xue Yuan Pei, Rajeev Misra, Ben Luisi

Journal:

Year:

2008

Language:

english

File:

PDF, 1.15 MB

english, 2008

42

Polygalacturonase inhibiting proteins: players in plant innate immunity?

Luca Federici, Adele Di Matteo, Juan Fernandez-Recio, Demetrius Tsernoglou, Felice Cervone

Journal:

Trends in Plant Science

Year:

2006

Language:

english

File:

PDF, 284 KB

english, 2006

43

Apoflavodoxin: Structure, stability, and FMN binding

Susana Maldonado, Anabel Lostao, María Pilar Irún, Juan Férnandez-Recio, Carlos Gustavo Genzor, Elena Begoña González, Jose Antonio Rubio, Alejandra Luquita, Fatna Daoudi, Javier Sancho

Journal:

Year:

1998

Language:

english

File:

PDF, 1.39 MB

english, 1998

44

Efficient Relaxation of Protein–Protein Interfaces by Discrete Molecular Dynamics Simulations

Emperador, Agusti, Solernou, Albert, Sfriso, Pedro, Pons, Carles, Gelpi, Josep Lluis, Fernandez-Recio, Juan, Orozco, Modesto

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.08 MB

english, 2013

45

The Crystal Structure of the BAR Domain from Human Bin1/Amphiphysin II and Its Implications for Molecular Recognition †

Casal, Eva, Federici, Luca, Zhang, Wei, Fernandez-Recio, Juan, Priego, Eva-Maria, Miguel, Ricardo Nuñez, DuHadaway, James B., Prendergast, George C., Luisi, Ben F., Laue, Ernest D.

Journal:

Year:

2006

Language:

english

File:

PDF, 1.18 MB

english, 2006

46

Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges

Pallara, Chiara, Jiménez-García, Brian, Pérez-Cano, Laura, Romero-Durana, Miguel, Solernou, Albert, Grosdidier, Solène, Pons, Carles, Moal, Iain H., Fernandez-Recio, Juan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1.09 MB

english, 2013

47

Intermolecular Contact Potentials for Protein–Protein Interactions Extracted from Binding Free Energy Changes upon Mutation

Moal, Iain H., Fernandez-Recio, Juan

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.78 MB

english, 2013

48

The scoring of poses in protein-protein docking: current capabilities and future directions

Moal, Iain H, Torchala, Mieczyslaw, Bates, Paul A, Fernández-Recio, Juan

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 900 KB

english, 2013

49

Antihypertensive effects of lactoferrin hydrolyzates: Inhibition of angiotensin- and endothelin-converting enzymes

Fernández-Musoles, Ricardo, Salom, Juan B., Martínez-Maqueda, Daniel, López-Díez, José Javier, Recio, Isidra, Manzanares, Paloma

Journal:

Year:

2013

Language:

english

File:

PDF, 452 KB

english, 2013

50

Physical activity program for patients with dementia and their relative caregivers: randomized clinical trial in Primary Health Care (AFISDEMyF study)

Rodriguez-Sánchez, Emiliano, Criado-Gutiérrez, José, Mora-Simón, Sara, Muriel-Diaz, M, Gómez-Marcos, Manuel A, Recio-Rodríguez, José I, Patino-Alonso, M, Valero-Juan, Luis F, Maderuelo-Fernandez, José

Journal:

Year:

2014

Language:

english

File:

PDF, 275 KB

english, 2014

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