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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

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Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains

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Structural and energy determinants in protein-RNA docking

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Modeling binding affinity of pathological mutations for computational protein design

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

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

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

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Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems

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LightDock: A new multi-scale approach to protein-protein docking

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Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases

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

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Structural and computational characterization of disease-related mutations involved in protein-protein interfaces

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

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L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction

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Structural Characterization of Protein–Protein Interactions with pyDockSAXS

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PyDockEneRes: Per-residue decomposition of protein-protein docking energy

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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

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Docking-based identification of small-molecule binding sites at protein-protein interfaces

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Docking approaches for modeling multi-molecular assemblies

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

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Structural basis for the dominant or recessive character of GLIALCAM mutations found in leukodystrophies

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Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution

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PirePred: An Accurate Online Consensus Tool to Interpret Newborn Screening–Related Genetic Variants in Structural Context

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Novel treatment strategy for NRAS-mutated melanoma through a selective inhibitor of CD147/VEGFR-2 interaction

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Architecture of the ESCPE-1 membrane coat

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

research line

Single-cell and spatial omics

Single-cell and spatial omics encompass a set of advanced technologies and analytical approaches that profile...

research line

Cell type markers and single-cell data analysis

Cell type markers and single-cell data analysis focus on identifying genes, proteins, or molecular signatures...

research line

Protein interactions and network molecular biology

Protein interactions and network molecular biology focuses on understanding how proteins interact with each other...

research line

Cancer Genomics and Transcriptomics

Cancer Genomics and Transcriptomics is a multidisciplinary field that investigates both the DNA-level alterations and...

researcher

Jose-Jesus Fernandez

researcher

ajaskolowski

researcher

manolofernandez

researcher

Franciscoandujar

researcher

cgallego

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PharaohFUN: phylogenomic analysis for plant protein history and function elucidation

service unit

Bioinformatics unit at ibs.GRANADA

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Emerging human health concerns from chronic exposure to pesticide mixtures

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Distribution of y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala

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Modulation of the endogenous antioxidants paraoxonase-1 and urate by pesticide exposure and genetic variants of xenobiotic-metabolizing enzymes

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Activity and determinants of cholinesterases and paraoxonase-1 in blood of workers exposed to non-cholinesterase inhibiting pesticides

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Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth

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A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health

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Evaluation of Polyphenol Intake in Pregnant Women from South-Eastern Spain and the Effect on Anthropometric Measures at Birth and Gestational Age

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Transcriptomic profiling unveils novel therapeutic options for drug-resistant temporal lobe epilepsy

researcher

Antonio Gómez Martín

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Enrichment of Artemia nauplii in essential fatty acids with different types of liposomes and their use in the rearing of gilthead sea bream (Sparus aurata) larvae

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Differential metabolic and gene expression profile of juvenile common dentex (Dentex dentex L.) and gilthead sea bream (Sparus aurata L.) in relation to redox homeostasis

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Bacteria associated with winter mortalities in laboratory-reared common dentex (Dentex dentex L.)

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Differential tissue expression of uncoupling proteins in gilthead sea bream (Sparus aurata L): Lessons from UCP1 and UCP3 in fish

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Confinement exposure induces glucose regulated protein 75 (GRP75/mortalin/mtHsp70/PBP74/HSPA9B) in the hepatic tissue of gilthead sea bream (Sparus aurata L.)

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The time course of fish oil wash-out follows a simple dilution model in gilthead sea bream (Sparus aurata L.) fed graded levels of vegetable oils

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Gene expression survey of mitochondrial uncoupling proteins (UCP1/UCP3) in gilthead sea bream (Sparus aurata L.)

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Molecular characterization and expression analysis of six peroxiredoxin paralogous genes in gilthead sea bream (Sparus aurata): Insights from fish exposed to dietary, pathogen and confinement stressors

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Modelling the predictable effects of dietary lipid sources on the fillet fatty acid composition of one-year-old gilthead sea bream (Sparus aurata L.)

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Feed restriction up-regulates uncoupling protein 3 (UCP3) gene expression in heart and red muscle tissues of gilthead sea bream (Sparus aurata L.) New insights in substrate oxidation and energy expenditure

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Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility

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Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts

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Tissue-specific gene expression and functional regulation of uncoupling protein 2 (UCP2) by hypoxia and nutrient availability in gilthead sea bream (Sparus aurata): implications on the physiological significance of UCP1-3 variants

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Metabolic and transcriptional responses of gilthead sea bream (Sparus aurata L.) to environmental stress: New insights in fish mitochondrial phenotyping

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Effects of a silver nanomaterial on cellular organelles and time course of oxidative stress in a fish cell line (PLHC-1)

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Tissue-specific gene expression and fasting regulation of sirtuin family in gilthead sea bream (Sparus aurata)

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Negligible cytotoxicity induced by different titanium dioxide nanoparticles in fish cell lines

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Induction of EROD and BFCOD activities in tissues of barbel (Barbus callensis) from a water reservoir in Algeria

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Fish cell lines as a tool for the ecotoxicity assessment and ranking of engineered nanomaterials

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Gene expression profiling of whole blood cells supports a more efficient mitochondrial respiration in hypoxia-challenged gilthead sea bream (Sparus aurata)

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Acute hazard of biocides for the aquatic environmental compartment from a life-cycle perspective