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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

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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