Research Group

Detalle de: Structural Bioinformatics, Modeling and Biological Mechanisms

Title	Structural Bioinformatics, Modeling and Biological Mechanisms
Description	The group is focused to the theoretical study of biological phenomena at molecular level and the development of computer tools for the analysis, structural prediction and characterization of protein interactions, with key contributions in the field, like the ASA-based desolvation description, later implemented in other docking methods, or the pyDock docking and scoring program. The group consistently ranks highly in the CASP and CAPRI international blind assessment experiments, which shows the competitive capabilities of the computer tools developed in the group. The group is actively involved in many multi-disciplinary collaborative projects for the study of protein interactions of biomedical and biotechnological interest, with applications to practical challenges such as the interpretation of genetic variants and the identification of small-molecule modulators of protein interactions.
Home Page	https://model3dbio.csic.es/
Contact Email	juan.fernandezrecio@icvv.es
Collaborating Companies	Nostrumbiodiscovery. VIVEbiotech.
Spin Off
Patents	1.\tYraola, F., García-Vicente, S., Fernandez-Recio, J., Albericio, F., Zorzano, A., Royo, M., Marti, L. (2007) META-XYLYLENEDIAMINE VANADATE SALTS. Intl. Application # PCT/EP2007/054668; Publication # WO 2007 131996. Priority country: Intl. (US) 2.\tMourah, S., Villoutreix, B., Khayati, F., Menashi, S., Lebbe, C., Fernández-Recio, J., Calvo, F. (2016) POLYPEPTIDES FOR THE TREATMENT OF ANGIOGENESIS OR LYMPHANGIOGENESIS-RELATED DISEASES. Intl. Application # PCT/EP2015/077555; Publication # WO 2016/083409. Priority country: Intl. (US)
Hpc Resources	Hidalgo, CESGA, BSC
Institution	ICVV
Ontology	Omics, Computational Methods, Resources, Data Analysis, Artificial Intelligence, Machine Learning in Biology, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.), Applications of Computational Biology, Structural bioinformatics, Molecular flexibility, Computational models and simulations, Biosystems Modeling, Statistical Methods for Biology, Mutation Analysis and design, Proteomics, Multivariate statistics, Biomolecular simulation, Structure-function relationship, Drug Discovery and design, Structure prediction, Molecular Interactions/Docking, Protein-Protein Interactions, Bayesian statistics, Population dynamics, Protein/Nucleic Acid design, Structural genomics
Tools	pyDockDNA, pyDock
Service Units	Cellular, Molecular and Bioinformatics Service at ICVV
Research Lines	New AI-based methods for the structural modeling of protein assemblies: integration of pyDock and AlphaFold, Development of new methodology for the energetic description of protein interactions, Molecular modeling of biological processes and mechanisms, Multi-scale of complex biological data in One Health
Funded Projects	NEW METHODS FOR BIOLOGICAL MODELING: PROTEIN INTERACTIONS, MUTATIONS, POLYPHENOLS AND HEALTH (BIOMODELPROT), NUEVAS TECNOLOGÍAS DIGITALES Y DE PROTEÍNAS EN PROCESOS DE VINIFICACIÓN PARA ABORDAR LOS RETOS DEL SECTOR ENOLÓGICO EN EL TERRITORIO POCTEFA (OENOPROT), BIOINFORMÁTICA, ANÁLISIS DE DATOS Y MODELIZACIÓN PARA EL AVANCE DE LA VITIVINICULTURA, ONETICK: AN INTEGRATED ONE HEALTH APPROACH FOR PREVENTION, DETECTION AND TREATMENT OF TICK-BORNE DISEASES IN URBAN AND PERI-URBAN ENVIRONMENTS, GRUPO DE INVESTIGACIÓN RECONOCIDO BIOINFORMATICA ESTRUCTURAL, MODELADO Y MECANISMOS BIOLOGICOS
Selected Publications	Structural vulnerability in EPCR suggests functional modulation Article · 31 Jan 2024 Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment Article · 31 Oct 2023 Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study Article · 27 Jun 2023 Architecture of the ESCPE-1 membrane coat Article · 15 Jun 2023 pyDockDNA: A new web server for energy-based protein-DNA docking and scoring Software · 6 Oct 2022 View all (125 more) Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution Article · 25 Aug 2022 PirePred: An Accurate Online Consensus Tool to Interpret Newborn Screening–Related Genetic Variants in Structural Context Article · Apr 2022 Novel treatment strategy for NRAS-mutated melanoma through a selective inhibitor of CD147/VEGFR-2 interaction Article · 26 Feb 2022 PDBe-KB: collaboratively defining the biological context of structural data Article · 10 Nov 2021 Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment Article · 13 Sep 2021 New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes Article · 27 Mar 2021 Docking approaches for modeling multi-molecular assemblies Article · Oct 2020 UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes Article · 6 Aug 2020 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 Article · 11 Jun 2020 Structural basis for the dominant or recessive character of GLIALCAM mutations found in leukodystrophies Article · 21 Jan 2020 Docking-based identification of small-molecule binding sites at protein-protein interfaces Article · Jan 2020 Structural Characterization of Protein–Protein Interactions with pyDockSAXS Book / chapter · 2020 Modeling of Protein Complexes and Molecular Assemblies with pyDock Book / chapter · 2020 PyDockEneRes: Per-residue decomposition of protein-protein docking energy Article · 6 Dec 2019 Integrative modeling of protein‐protein interactions with pyDock for the new docking challenges Article · 30 Nov 2019 Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment Article · 25 Oct 2019 L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction Article · 18 Apr 2019 Structural and computational characterization of disease-related mutations involved in protein-protein interfaces Article · 29 Mar 2019 Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases Article · 7 Aug 2018 SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation Article · 18 Jul 2018 Hot-spot analysis for drug discovery targeting protein-protein interactions Article · 29 Jan 2018 Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems Book / chapter · 2018 Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains Article · 13 Nov 2017 LightDock: A new multi-scale approach to protein-protein docking Article · 4 Sep 2017 Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations Article · 25 Aug 2017 A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining Article · 12 Apr 2017 Structural and energy determinants in protein-RNA docking Article · Apr 2017 IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection Article · 14 Feb 2017 Modeling binding affinity of pathological mutations for computational protein design Book / chapter · 3 Dec 2016 pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo-multimers, and domain–domain interactions Article · 25 Oct 2016 Optimization of protein-protein docking for predicting Fc-protein interactions Article · 22 Jul 2016 Unraveling the molecular details of the innate immune response Article · Jul 2016 Conformational heterogeneity of unbound proteins enhances recognition in protein-protein encounters Article · 28 Jun 2016 Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment Article · Jun 2016 Interaction of photosystem i from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor Article · Dec 2015 Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2 Article · Sep 2015 Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction Article · Sep 2015 PyDockSAXS: Protein-protein complex structure by SAXS and computational docking Article · 20 Apr 2015 Inferring the microscopic surface energy of protein-protein interfaces from mutation data Article · 5 Feb 2015 Comment on 'protein-protein binding affinity prediction from amino acid sequence' Article · 17 Oct 2014 CCharPPI web server: Computational characterization of protein-protein interactions from structure Article · 2 Sep 2014 Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5 Article · 11 Aug 2014 Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity Article · 13 Apr 2014 Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc Article · 10 Feb 2014 Scoring functions for protein-protein interactions Article · Dec 2013 Blind prediction of interfacial water positions in CAPRI Article · 23 Nov 2013 Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges Article · 17 Oct 2013 The scoring of poses in protein-protein docking: Current capabilities and future directions Article · 1 Oct 2013 Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization Article · 5 Sep 2013 Conformational transitions in human translin enable nucleic acid binding Article · 26 Aug 2013 Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions Article · 23 Aug 2013 Intermolecular contact potentials for protein-protein interactions extracted from binding free energy changes upon mutation Article · 3 Jul 2013 Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD Article · 16 May 2013 pyDockWEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring Article · 9 May 2013 Validated conformational ensembles are key for the successful prediction of protein complexes Article · 4 Mar 2013 SwarmDock: A server for flexible protein-protein docking Article · 23 Jan 2013 Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations Article · 28 Dec 2012 Protein-protein docking and hot-spot prediction for drug discovery Article · 23 Aug 2012 SKEMPI: A Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models Article · 1 Aug 2012 Cell-Dock: High-performance protein-protein docking Article · 19 Jul 2012 Allosteric conversation in the androgen receptor ligand-binding domain surfaces Article · Jul 2012 A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data Article · 8 May 2012 Theory and simulation: Complexity and emergence Article · Apr 2012 Established and emerging trends in computational drug discovery in the structural genomics era Article · Jan 2012 Community-wide assessment of protein-interface modeling suggests improvements to design methodology Article · Nov 2011 Prediction of protein-binding areas by small-world residue networks and application to docking Article · 26 Sep 2011 LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains Article · 18 Jul 2011 Prediction of protein binding sites and hot spots Article · 3 May 2011 PyDockCG: New coarse-grained potential for protein-protein docking Article · 21 Apr 2011 Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein docking Article · 7 Jan 2011 Drug design on the cell BE Other · 7 Dec 2010 Dissection and prediction of RNA-binding sites on proteins Article · 1 Dec 2010 Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data Article · Oct 2010 Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation Article · 28 Jun 2010 Interdomain conformations in the full-length MMP-2 enzyme explored by protein-protein docking calculations using pyDock Article · 28 Jun 2010 The 4th meeting on the Critical Assessment of PRedicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona Article · 14 Jun 2010 Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding Article · 20 May 2010 Theory and simulation: integrating models into experimental scenarios Article · Apr 2010 Mapping of interaction sites of the Schizosaccharomyces pombe protein translin with nucleic acids and proteins: A combined molecular genetics and bioinformatics study Article · 15 Jan 2010 Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine Article · 2010 Present and future chanllenges and limitations in protein-Protein clocking Article · 27 Nov 2009 Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins Article · 27 Nov 2009 Pushing structural information into the yeast interactome by high-throughput protein docking experiments Article · 28 Aug 2009 Docking and scoring: Applications to drug discovery in the interactomics era Article · 21 May 2009 Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein Article · 5 May 2009 Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering Article · 25 Mar 2009 Predicting protein protein interfaces as clusters of Optimal Docking Area points Article · 2009 Identification of hot-spot residues in protein-protein interactions by computational docking Article · 21 Oct 2008 Structural assembly of two-domain proteins by rigid-body docking Article · 16 Oct 2008 Docking of cytochrome c6 and plastocyanin to the aa 3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum Article · 29 Sep 2008 Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid) Article · 18 Jun 2008 Editorial Article · Apr 2008 Assembly and Channel Opening in a Bacterial Drug Efflux Machine Article · Apr 2008 In silico docking of urokinase plasminogen activator and integrins Article · Mar 2008 Docking analysis of transient complexes: Interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin Article · 7 Feb 2008 Prediction and scoring of docking poses with pyDock Article · 31 Oct 2007 The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane Article · Oct 2007 Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase- inhibiting proteins Article · 17 Sep 2007 PyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking Software · 19 Apr 2007 Structural and functional characterization of binding sites in metallocarboxypeptidases based on optimal docking area analysis Article · 3 Apr 2007 Recognition and Cooperation Between the ATP-dependent RNA Helicase RhlB and Ribonuclease RNase E Article · Mar 2007 Identifying interaction motifs in CK2β - a ubiquitous kinase regulatory subunit Article · Dec 2006 Cell biology: Brief encounters bolster contacts Article · Nov 2006 New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: Analysis by SARs and computational docking Article · 22 Sep 2006 Predicting protein-protein interface using desolvation energy similarity matching Conference paper · Sep 2006 Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment Article · Apr 2006 Polygalacturonase inhibiting proteins: Players in plant innate immunity? Article · Feb 2006 Data mining of molecular dynamic trajectories of nucleic acids Book / chapter · 2006 The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea Article · 21 Oct 2005 Improving CAPRI predictions: Optimized desolvation for rigid-body docking Article · 24 Jun 2005 The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 Å resolution Article · Apr 2005 A model of a transmembrane drug-efflux pump from Gram-negative bacteria Article · 18 Nov 2004 The long and short flavodoxins: II. The role of the differentiating loop in apoflavodoxin stability and folding mechanism Article · Nov 2004 Optimal docking area: A new method for predicting protein-protein interaction sites Article · 19 Oct 2004 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 Article · 25 Dec 2003 ICM-DISCO docking by global energy optimization with fully flexible side-chains Article · 14 May 2003 Soft protein-protein docking in internal coordinates Article · Feb 2002 Apoflavodoxin folding mechanism: An α/β protein with an essentially off-pathway intermediate Article · 21 Nov 2001 Modulation of electroenzymatic NADPH oxidation through oriented immobilization of ferredoxin:NADP+ reductase onto modified gold electrodes Article · 23 Sep 2000 Energetics of a hydrogen bond (charged and neutral) and of a cation-π interaction in apoflavodoxin Article · Jul 1999 Investigation of the diaphorase reaction of ferredoxin-NADP+ reductase by electrochemical methods Article · Nov 1998 Apoflavodoxin: Structure, stability, and FMN binding Article · Oct 1998 Intrahelical side chain interactions in α-helices: Poor correlation between energetics and frequency Article · 5 Jun 1998 Corrigendum: The tryptophan/histidine interaction in α-helices (J. Mol. Biol. (1997) 267 (184-197)) Article · Jul 1997 The Tryptophan/Histidine interaction in α-helices Article · Mar 1997
Researchers	Luis Ángel Rodríguez Lumbreras, Víctor Monteagudo Honrubia, Juan Fernández Recio, Luis García Aguirre, Rafael Torres Pérez

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