Juan Fernández-Recio

发表

Present and future challenges and limitations in protein–protein docking

Carles Pons, Solène Grosdidier, Albert Solernou, 2010, Proteins.

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

Zhiping Weng, Mieczyslaw Torchala, Juan Fernández-Recio, 2017, Bioinform..

pyDockEneRes: per-residue decomposition of protein-protein docking energy

Juan Fernández-Recio, Brian Jiménez-García, Miguel Romero-Durana, 2019, Bioinform..

Computational modeling of protein interactions for biomedical applications

Juan Fernández-Recio, 2018 .

pyDock performance in 5th CAPRI edition: from docking and scoring to binding affinity predictions and other challenges

Juan Fernández-Recio, Brian Jiménez-García, Chiara Pallara, 2015 .

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

Juan Fernández-Recio, Tom L. Blundell, Tammy M. K. Cheng, 2008, BMC Bioinformatics.

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Juan Fernández-Recio, Iain H. Moal, J. Fernández-Recio, 2012, Bioinform..

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

Juan Fernández-Recio, Patrick Aloy, Roberto Mosca, 2009, PLoS Comput. Biol..

Computer applications for prediction of protein-protein interactions and rational drug design.

Solène Grosdidier, Juan Fernández-Recio, Max Totrov, 2009, Advances and applications in bioinformatics and chemistry : AABC.

Docking through democracy re-ranking protein-protein decoys with a voting system

Juan Fernández-Recio, Iain H. Moal, Didier Barradas-Bautista, 2015 .

Optimized Desolvation for Rigid-Body Docking: Fast Prediction of Protein Interaction Sites

Juan Fernández-Recio, 2004, Spanish Bioinformatics Conference.

Prediction and scoring of docking poses with pyDock

Solène Grosdidier, Albert Solernou, Juan Fernández-Recio, 2007, Proteins.

Structural Characterization of Protein-Protein Interactions with pyDockSAXS.

Juan Fernández-Recio, Brian Jiménez-García, Pau Bernadó, 2020, Methods in molecular biology.

Scoring functions for protein-protein interactions.

David Baker, Juan Fernández-Recio, Rocco Moretti, 2013, Current opinion in structural biology.

Pacific Symposium on Biocomputing 15:269-280(2010) STRUCTURAL PREDICTION OF PROTEIN-RNA INTERACTION BY COMPUTATIONAL DOCKING WITH PROPENSITY-BASED STATISTICAL POTENTIALS

Carles Pons, Albert Solernou, Juan Fernández-Recio, 2022 .

pyDockDNA: a new approach for protein-DNA docking

Juan Fernández-Recio, Brian Jiménez-García, Luis Ángel Rodríguez-Lumbreras, 2017 .

Computational Tools for Exploration of the Energy Landscape in Protein‐Protein Association

Albert Solernou, Juan Fernández-Recio, 2008 .

Refinement of rigid-body protein–protein docking using backbone and side-chain minimization with a coarse-grained model

Albert Solernou, Juan Fernández-Recio, J. Fernández-Recio, 2010 .

Theory and simulation: complexity and emergence.

Juan Fernández-Recio, Chandra Verma, 2012, Current opinion in structural biology.

Cell-Dock: high-performance protein-protein docking

Harald Servat, Daniel Jiménez-González, Carles Pons, 2012, Bioinform..

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

Theory and simulation. Editorial overview.

Juan Fernández-Recio, Chandra Verma, 2008, Current opinion in structural biology.

Protein-protein docking and hot-spot prediction for drug discovery.

Juan Fernández-Recio, Solene Grosdidier, 2012, Current pharmaceutical design.

pyDockSAXS: protein–protein complex structure by SAXS and computational docking

Dmitri I. Svergun, Carles Pons, Juan Fernández-Recio, 2015, Nucleic Acids Res..

Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization

Mieczyslaw Torchala, Juan Fernández-Recio, Iain H. Moal, 2013, PLoS Comput. Biol..

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring

Carles Pons, Juan Fernández-Recio, Brian Jiménez-García, 2013, Bioinform..

In silico docking of urokinase plasminogen activator and integrins

Juan Fernández-Recio, Maria Vittoria Cubellis, Valentina Citro, 2008, BMC Bioinformatics.

pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions

Juan Fernández-Recio, Brian Jiménez-García, Chiara Pallara, 2017, Proteins.

CCharPPI web server: computational characterization of protein-protein interactions from structure

Juan Fernández-Recio, Iain H. Moal, Brian Jiménez-García, 2015, Bioinform..

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

Mieczyslaw Torchala, Juan Fernández-Recio, Iain H. Moal, 2013, BMC Bioinformatics.

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

Juan Fernández-Recio, Fabian Glaser, Carles Pons, 2011, BMC Bioinformatics.

Predicting protein - protein interfaces as clusters of Optimal Docking Area points

Joarder Kamruzzaman, Gour C. Karmakar, Juan Fernández-Recio, 2009, Int. J. Data Min. Bioinform..

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

Albert Solernou, Juan Fernández-Recio, 2009, BMC Bioinformatics.

A systematic analysis of scoring functions in rigid‐body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining

Juan Fernández-Recio, Didier Barradas-Bautista, Iain H Moal, 2017, Proteins.

SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

Juan Fernández-Recio, Iain H. Moal, Brian Jiménez-García, 2018, bioRxiv.

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

Solène Grosdidier, Juan Fernández-Recio, J. Fernández-Recio, 2008, BMC Bioinformatics.

Comment on 'protein-protein binding affinity prediction from amino acid sequence'

Juan Fernández-Recio, Iain H. Moal, J. Fernández-Recio, 2015, Bioinform..

Drug Design on the Cell BE

Harald Servat, Daniel Jiménez-González, Carles Pons, 2010, Scientific Computing with Multicore and Accelerators.

UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes

Victor Guallar, Juan Fernández-Recio, Pep Amengual-Rigo, 2020, Bioinform..

Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching

Joarder Kamruzzaman, Gour C. Karmakar, Juan Fernández-Recio, 2006, 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

LightDock: a new multi-scale approach to protein–protein docking

Daniel Jiménez-González, Juan Fernández-Recio, Brian Jiménez-García, 2018, Bioinform..

FRODOCK: a new approach for fast rotational protein-protein docking

Ruben Abagyan, Carles Pons, Juan Fernández-Recio, 2009, Bioinform..

Prediction of protein binding sites and hot spots

Juan Fernández-Recio, J. Fernández-Recio, 2011 .

Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study

Laura Pérez-Cano, Juan Fernández-Recio, Fabian Glaser, 2010, Nucleic acids research.

Dissection and prediction of RNA-binding sites on proteins

Laura Pérez-Cano, Juan Fernández-Recio, L. Perez-Cano, 2010, Biomolecular concepts.

SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation

Juan Fernández-Recio, Iain H. Moal, Brian Jiménez-García, 2018, bioRxiv.

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

Laura Pérez-Cano, Juan Fernández-Recio, Brian Jiménez-García, 2012, Proteins.

Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters.

Ruben Abagyan, Juan Fernández-Recio, Chiara Pallara, 2016, Journal of chemical theory and computation.

Modeling Binding Affinity of Pathological Mutations for Computational Protein Design.

Juan Fernández-Recio, Fabian Glaser, Miguel Romero-Durana, 2017, Methods in molecular biology.

Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment.

Juan Fernández-Recio, Tom L Blundell, Vijayalakshmi Chelliah, 2006, Journal of molecular biology.

Inferring the microscopic surface energy of protein–protein interfaces from mutation data

Juan Fernández-Recio, Iain H Moal, Justas Dapkūnas, 2015, Proteins.

Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.

Dmitri I Svergun, Juan Fernández-Recio, Modesto Orozco, 2010, Journal of molecular biology.

The Tryptophan/Histidine interaction in α-helices

Juan Fernández-Recio, Javier Sancho, Paz Sevilla, 1997 .

Allosteric conversation in the androgen receptor ligand-binding domain surfaces.

Solène Grosdidier, Juan Fernández-Recio, Phuong Nguyen, 2012, Molecular endocrinology.

Assembly and Channel Opening in a Bacterial Drug Efflux Machine

Nicholas Furnham, Laura Pérez-Cano, Juan Fernández-Recio, 2008, Molecular cell.

Docking and scoring: applications to drug discovery in the interactomics era

Solène Grosdidier, Juan Fernández-Recio, J. Fernández-Recio, 2009, Expert opinion on drug discovery.

Cell biology: Brief encounters bolster contacts

Juan Fernández-Recio, Tom L. Blundell, T. Blundell, 2006, Nature.

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

Daniel Fernández, Juan Fernández-Recio, Josep Vendrell, 2007, Proteins.