List of works - Juan Fernández-Recio

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

scientific article published in December 2004

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

scientific article

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

scientific article published on 25 March 2017

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

scientific article

Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction

scientific article

Apoflavodoxin folding mechanism: an alpha/beta protein with an essentially off-pathway intermediate

scientific article published in December 2001

Apoflavodoxin: Structure, stability, and FMN binding

scientific article published on 01 October 1998

Assembly and Channel Opening in a Bacterial Drug Efflux Machine

scientific article

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

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

scientific article published on 02 September 2014

Cell biology: brief encounters bolster contacts.

scientific article

Cell-Dock: high-performance protein-protein docking.

scientific article published on 19 July 2012

Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization

scientific article (publication date: 2013)

Comment on ‘protein–protein binding affinity prediction from amino acid sequence’

scientific article published on 17 October 2014

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

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Conformational transitions in human translin enable nucleic acid binding.

scientific article published on 26 August 2013

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

scientific article

Data Mining of Molecular Dynamic Trajectories of Nucleic Acids

Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid)

scientific article

Dissection and prediction of RNA-binding sites on proteins.

scientific article

Diverging co-translational protein complex assembly pathways are governed by interface energy distribution

scientific article published in 2024

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

scientific article

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

scientific article published in June 2009

Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum

scientific article published on 29 September 2008

Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations.

scientific article published on 25 August 2017

Editorial

scientific article published on 10 April 2008

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

scientific article published on 28 December 2012

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

scientific article

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

scientific article

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

scientific article published on January 27, 2012

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

scientific article published on 17 October 2013

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

scientific article published on 20 July 2009

Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine

scientific article published on 4 January 2010

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

scientific article published in July 2003

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

scientific article

Identification of protein-protein interaction sites from docking energy landscapes

scientific article published in January 2004

Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit

scientific article

Improving CAPRI predictions: optimized desolvation for rigid-body docking

scientific article published in August 2005

In silico docking of urokinase plasminogen activator and integrins

scientific article

Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

scientific article published on 5 February 2015

Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein

scholarly article

Integrative modeling of protein-protein interactions with pyDock for the new docking challenges

scientific article published on 19 November 2019

Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor

scientific article published on 22 September 2015

Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein-Protein Docking Calculations Using pyDock

scientific article published on July 2010

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

scientific article published on 3 July 2013

Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency

scientific article published in June 1998

Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases

scientific article published in Scientific Reports

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

LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains

scientific article

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

scientific article published on 15 January 2010

Modelling the evolution of COVID-19 in high-incidence European countries and regions: estimated number of infections and impact of past and future intervention measures

scientific article published on 13 May 2020

New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: analysis by SARs and computational docking

scientific article published in October 2006

Optimal docking area: a new method for predicting protein-protein interaction sites

scientific article published in January 2005

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

scientific article published in January 2010

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

scientific article published in November 2010

Polygalacturonase inhibiting proteins: players in plant innate immunity?

article

Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching

Predicting protein-protein interfaces as clusters of optimal docking area points.

scientific article published in January 2009

Prediction and scoring of docking poses with pyDock

scientific article published in December 2007

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

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

scientific article

Present and future challenges and limitations in protein-protein docking

scientific article

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

scientific article

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

scientific article published on January 2012

Pushing structural information into the yeast interactome by high-throughput protein docking experiments

scientific article

Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.

scientific article

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

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

scientific article published on August 2012

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking

scientific article published on 07 January 2011

Scoring functions for protein–protein interactions ⬇️

scientific article published on July 18, 2013

Soft protein–protein docking in internal coordinates ⬇️

scientific article published on February 1, 2002

Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD

scientific article

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

scientific article published in July 2007

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

scientific article

Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc.

scientific article published on 10 February 2014

Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.

scientific article

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

scientific article

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

scientific article published on April 2009

SwarmDock: a server for flexible protein-protein docking

scientific article published on 23 January 2013

Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity

scientific article published on 13 April 2014

The Tryptophan/Histidine interaction in α-helices

scientific article published on 01 March 1997

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

scientific article

The crystal structure of the BAR domain from human Bin1/amphiphysin II and its implications for molecular recognition

scientific article published in October 2006

The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 A resolution.

scientific article

The long and short flavodoxins: II. The role of the differentiating loop in apoflavodoxin stability and folding mechanism

scientific article

The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea

scientific article published on 21 October 2005

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

scientific article

The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane

scientific article

Theory and simulation: complexity and emergence

scientific article published on 12 March 2012

Theory and simulation: integrating models into experimental scenarios

scientific article published on 11 March 2010

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

scientific article

Validated Conformational Ensembles Are Key for the Successful Prediction of Protein Complexes

scientific article published on 4 March 2013

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

scientific article published on 4 October 2016

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

scientific article published on 01 August 2007

pyDockCG: new coarse-grained potential for protein-protein docking

scientific article published on 21 April 2011

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

scientific article published on May 9, 2013

List of works by Juan Fernández-Recio

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

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

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

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

Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction

Apoflavodoxin folding mechanism: an alpha/beta protein with an essentially off-pathway intermediate

Apoflavodoxin: Structure, stability, and FMN binding

Assembly and Channel Opening in a Bacterial Drug Efflux Machine

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Blind prediction of interfacial water positions in CAPRI

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

Cell biology: brief encounters bolster contacts.

Cell-Dock: high-performance protein-protein docking.

Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization

Comment on ‘protein–protein binding affinity prediction from amino acid sequence’

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

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Conformational transitions in human translin enable nucleic acid binding.

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

Data Mining of Molecular Dynamic Trajectories of Nucleic Acids

Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid)

Dissection and prediction of RNA-binding sites on proteins.

Diverging co-translational protein complex assembly pathways are governed by interface energy distribution

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

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

Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum

Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations.

Editorial

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

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

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

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

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

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

Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine

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

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

Identification of protein-protein interaction sites from docking energy landscapes

Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit

Improving CAPRI predictions: optimized desolvation for rigid-body docking

In silico docking of urokinase plasminogen activator and integrins

Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein

Integrative modeling of protein-protein interactions with pyDock for the new docking challenges

Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor

Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein-Protein Docking Calculations Using pyDock

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

Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency

Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases

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

LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains

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

Modelling the evolution of COVID-19 in high-incidence European countries and regions: estimated number of infections and impact of past and future intervention measures

New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: analysis by SARs and computational docking

Optimal docking area: a new method for predicting protein-protein interaction sites

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

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

Polygalacturonase inhibiting proteins: players in plant innate immunity?

Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching

Predicting protein-protein interfaces as clusters of optimal docking area points.

Prediction and scoring of docking poses with pyDock

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

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

Present and future challenges and limitations in protein-protein docking

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

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

Pushing structural information into the yeast interactome by high-throughput protein docking experiments

Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.

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

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

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking

Scoring functions for protein–protein interactions ⬇️

Soft protein–protein docking in internal coordinates ⬇️

Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD

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

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

Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc.

Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.

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