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Molecular modeling of biological processes and mechanisms

We are modeling the interaction of polyphenols with relevant targets in human health, like the...

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Development of new methodology for the energetic description of protein interactions

We are exploring the use of pyDock energy-based function to describe the energetics of protein-protein...

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New AI-based methods for the structural modeling of protein assemblies: integration of pyDock and AlphaFold

We are using AI-based methods like AlphaFold to improve structural modeling of protein-protein complexes. Our...

tool

pyDock

Protein-protein docking pipeline using FFT-based sampling and energy-based scoring.

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The Tryptophan/Histidine interaction in α-helices

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Corrigendum: The tryptophan/histidine interaction in α-helices (J. Mol. Biol. (1997) 267 (184-197))

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

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Intrahelical side chain interactions in α-helices: Poor correlation between energetics and frequency

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Apoflavodoxin: Structure, stability, and FMN binding

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

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Modulation of electroenzymatic NADPH oxidation through oriented immobilization of ferredoxin:NADP⁺ reductase onto modified gold electrodes

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Apoflavodoxin folding mechanism: An α/β protein with an essentially off-pathway intermediate

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Soft protein-protein docking in internal coordinates

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

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

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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

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

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

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

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

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Improving CAPRI predictions: Optimized desolvation for rigid-body docking

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Predicting protein-protein interface using desolvation energy similarity matching

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Polygalacturonase inhibiting proteins: Players in plant innate immunity?

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

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Identifying interaction motifs in CK2β - a ubiquitous kinase regulatory subunit

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

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Data mining of molecular dynamic trajectories of nucleic acids

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Cell biology: Brief encounters bolster contacts

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

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Structural and functional characterization of binding sites in metallocarboxypeptidases based on optimal docking area analysis

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

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

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Prediction and scoring of docking poses with pyDock

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

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In silico docking of urokinase plasminogen activator and integrins

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

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Editorial

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Docking of cytochrome c₆ and plastocyanin to the aa ₃-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum

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

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

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

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Assembly and Channel Opening in a Bacterial Drug Efflux Machine

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

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

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Predicting protein protein interfaces as clusters of Optimal Docking Area points

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

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

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Theory and simulation: integrating models into experimental scenarios

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

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

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

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Present and future chanllenges and limitations in protein-Protein clocking

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

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

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

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Interdomain conformations in the full-length MMP-2 enzyme explored by protein-protein docking calculations using pyDock

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

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Drug design on the cell BE

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Dissection and prediction of RNA-binding sites on proteins

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Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein docking

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PyDockCG: New coarse-grained potential for protein-protein docking

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

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Prediction of protein binding sites and hot spots

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

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

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Theory and simulation: Complexity and emergence

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

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

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Established and emerging trends in computational drug discovery in the structural genomics era

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Cell-Dock: High-performance protein-protein docking

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Allosteric conversation in the androgen receptor ligand-binding domain surfaces

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

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

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Validated conformational ensembles are key for the successful prediction of protein complexes

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

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SwarmDock: A server for flexible protein-protein docking

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

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Scoring functions for protein-protein interactions

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Intermolecular contact potentials for protein-protein interactions extracted from binding free energy changes upon mutation

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

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Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations

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Conformational transitions in human translin enable nucleic acid binding

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

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

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

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

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

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Blind prediction of interfacial water positions in CAPRI

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

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PyDockSAXS: Protein-protein complex structure by SAXS and computational docking

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

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

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

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

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

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Unraveling the molecular details of the innate immune response

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

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Optimization of protein-protein docking for predicting Fc-protein interactions

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Conformational heterogeneity of unbound proteins enhances recognition in protein-protein encounters

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