J. Bonet

发表

Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details

E. Guney, B. Oliva, O. Fornes, 2012, Molecular informatics.

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

B. Oliva, O. Fornes, G. de las Cuevas, 2021, NAR genomics and bioinformatics.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Matti Pirinen, Jukka Corander, Krister Wennerberg, 2016, Nature Communications.

On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions.

Oriol Fornes, Jaume Bonet, Javier Garcia-Garcia, 2014, Advances in protein chemistry and structural biology.

Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence

A. Gursoy, B. Oliva, J. Bonet, 2012 .

CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells.

G. Castellano, M. Beato, B. Oliva, 2012, Genes & development.

gene regulation in breast cancer cells CDK 2-dependent activation of PARP-1 is required for hormonal Material Supplemental

G. Castellano, M. Beato, B. Oliva, 2012 .

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin‐α7 mediated nuclear import pathway

B. Oliva, J. Bonet, Swantje Thiele, 2019, The FEBS journal.

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway

B. Oliva, J. Bonet, Swantje Thiele, 2018, bioRxiv.

De novo protein design enables precise induction of functional antibodies in vivo

B. Correia, P. Corthésy, J. Bates, 2020 .

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

S. Reddy, P. Gainza, B. Correia, 2018, bioRxiv.

Trivalent cocktail of de novo designed immunogens enables the robust induction and focusing of functional antibodies in vivo

Y. Li, P. Corthésy, X. Wen, 2019, bioRxiv.

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

P. Gainza, P. Corthésy, M. Chen, 2018, bioRxiv.

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

G. Coukos, B. Oh, P. Gainza, 2020, Nature Biotechnology.

Preclinical development of a humanized chimeric antigen receptor against B-cell maturation antigen for multiple myeloma

M. Juan, J. Bonet, N. Fernandez-Fuentes, 2020, Haematologica.

The role of residue stability in transient protein–protein interactions involved in enzymatic phosphate hydrolysis. A computational study

Michael A. Johnston, J. Teyra, J. Bonet, 2005, Proteins: Structure, Function, and Bioinformatics.

A bottom-up approach for the de novo design of functional proteins

Eva A. van Aalen, M. Fussenegger, M. Merkx, 2020, bioRxiv.

Intramolecular trimerization, a novel strategy for making multispecific antibodies with controlled orientation of the antigen binding domains

B. Oliva, L. Álvarez-Vallina, J. Bonet, 2016, Scientific Reports.

Prediction of a new class of RNA recognition motif

B. Oliva, F. Avilés, J. Bonet, 2011, Journal of molecular modeling.

Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions

J. Bonet, N. Fernandez-Fuentes, J. Aguirre-Plans, 2020, Protein science : a publication of the Protein Society.

The antigen-binding fragment of human gamma immunoglobulin prevents amyloid β-peptide folding into β-sheet to form oligomers

B. Oliva, J. Bonet, R. Vicente, 2017, Oncotarget.

Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease

B. Oliva, Javier García-García, J. Bonet, 2019, Computational and structural biotechnology journal.

Automated structure-based learning to model co-operativity and protein-DNA interactions in cis -regulatory modules

B. Oliva, O. Fornes, J. Bonet, 2022 .

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

B. Oliva, O. Fornes, J. Bonet, 2019, bioRxiv.

Elongation of the C-terminal domain of an anti-amyloid β single-chain variable fragment increases its thermodynamic stability and decreases its aggregation tendency

B. Oliva, J. Bonet, S. Villegas, 2013, mAbs.

ADP-ribose derived Nuclear ATP is Required for Chromatin Remodeling and Hormonal Gene Regulation (97 charact)

M. Beato, A. Pohl, B. Oliva, 2014, bioRxiv.

RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis

B. Oliva, O. Fornes, G. de las Cuevas, 2018, bioRxiv.

Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements

B. Oliva, O. Fornes, J. Bonet, 2022, bioRxiv.

Bispecific light T-cell engagers for gene-based immunotherapy of epidermal growth factor receptor (EGFR)-positive malignancies

L. Álvarez-Vallina, J. Bonet, F. Blanco, 2018, Cancer Immunology, Immunotherapy.

ATTACK, a novel bispecific T cell-recruiting antibody with trivalent EGFR binding and monovalent CD3 binding for cancer immunotherapy

L. Álvarez-Vallina, J. Bonet, F. Blanco, 2017, Oncoimmunology.

SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions

Oriol Fornes, Jaume Bonet, Narcis Fernandez-Fuentes, 2021, BMC Bioinform..

ModCRE: a structure homology-modeling approach to predict TF binding in cis -regulatory elements

O. Fornes, J. Bonet, J. Aguirre-Plans, 2022 .

RosettaSurf—A surface-centric computational design approach

P. Vandergheynst, Andreas Loukas, M. Defferrard, 2021, bioRxiv.

ADP-ribose–derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling

M. Beato, A. Pohl, B. Oliva, 2016, Science.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures

Baldomero Oliva, Javier García-García, Joan Planas-Iglesias, 2017, Bioinform..

Rosetta FunFolDes – A general framework for the computational design of functional proteins

Sarah Wehrle, Jaume Bonet, Thomas Krey, 2018, bioRxiv.

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

G. Coukos, B. Oh, P. Gainza, 2020, Nature Biotechnology.

A generic framework for hierarchical de novo protein design

B. Correia, J. Bonet, Zander Harteveld, 2022, bioRxiv.

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

Bruno E. Correia, Jaume Bonet, Zander Harteveld, 2019, BMC Bioinformatics.

rstoolbox: management and analysis of computationally designed structural ensembles

Andreas Scheck, Bruno E. Correia, Jaume Bonet, 2018, bioRxiv.

Understanding protein-protein interactions using local structural features.

Elisenda Feliu, Joan Planas-Iglesias, Baldo Oliva, 2013, Journal of molecular biology.

ArchDB 2014: structural classification of loops in proteins

Baldomero Oliva, Javier García-García, Joan Planas-Iglesias, 2013, Nucleic Acids Res..

Bottom-up de novo design of functional proteins with complex structural features

Eva A. van Aalen, M. Fussenegger, M. Merkx, 2021, Nature Chemical Biology.

Targeting Importin-α7 as a Therapeutic Approach against Pandemic Influenza Viruses

B. Oliva, J. Bonet, E. Fodor, 2015, Journal of Virology.

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications

Baldomero Oliva, András Fiser, Jaume Bonet, 2014, Bio Algorithms Med Syst..

Generation and characterization of monospecific and bispecific hexavalent trimerbodies

B. Oliva, L. Álvarez-Vallina, J. Bonet, 2013, mAbs.

In Vivo Tumor Targeting and Imaging with Engineered Trivalent Antibody Fragments Containing Collagen-Derived Sequences

B. Oliva, L. Álvarez-Vallina, J. Bonet, 2009, PloS one.

Multivalent antibodies: when design surpasses evolution.

Baldomero Oliva, Jaume Bonet, B. Oliva, 2010, Trends in biotechnology.

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Benjamin K. Mueller, J. Meiler, J. Crowe, 2021, Biochemistry.

Structure-based immunogen design — leading the way to the new age of precision vaccines

Jaume Bonet, Fabian Sesterhenn, Bruno E Correia, 2018, Current Opinion in Structural Biology.

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.

Oriol Fornes, Joan Planas-Iglesias, Jaume Bonet, 2016, Biochemical Society transactions.

A PD-L1/EGFR bispecific antibody combines immune checkpoint blockade and direct anti-cancer action for an enhanced anti-tumor response

L. Álvarez-Vallina, B. Blanco, J. Bonet, 2023, Oncoimmunology.

De novo protein design enables the precise induction of RSV-neutralizing antibodies

Luciano A. Abriata, John T. Bates, Bruno E. Correia, 2020, Science.

Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design

Baldomero Oliva, Joan Segura, Joan Planas-Iglesias, 2014, Bioinform..

Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential

Zhenyu Xu, J. Bonet, Slawomir Kubik, 2021, bioRxiv.

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

Marc A. Martí-Renom, Baldomero Oliva, Andrej Sali, 2007, PLoS Comput. Biol..

Amyloid-β Peptide Nitrotyrosination Stabilizes Oligomers and Enhances NMDAR-Mediated Toxicity

N. Inestrosa, B. Oliva, J. Bonet, 2016, The Journal of Neuroscience.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Karen R. Khar, Roland L. Dunbrack, 2020, Nature Methods.

iLoops: a protein-protein interaction prediction server based on structural features

Baldomero Oliva, Javier García-García, Joan Planas-Iglesias, 2013, Bioinform..

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Suleiman A. Khan, Michael A. Goren, Donna E. Dillenberger, 2016, Nature Communications.