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Jaume Bonet Martinez

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Related publications (21)

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

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Stéphane Rosset, Fabian Sesterhenn, Andreas Scheck, Sarah Wehrle, Che Yang, Freyr Sverrisson, Sabrina Susan Vollers, Mélanie Evelyne Villard

The robust computational design of functional proteins has the potential to deeply impact translational research and broaden our understanding of the determinants of protein function and stability. The low success rates of computational design protocols an ...

2018

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

Jaume Bonet Martinez

Multiple myeloma is a prevalent and incurable disease, despite the development of new and effective drugs. The recent development of chimeric antigen receptor (CAR)T cells has shown impressive results in the treatment of patients with relapsed or refractor ...

FERRATA STORTI FOUNDATION2021

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

Jaume Bonet Martinez

BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...

2021

RosettaSurf-A surface-centric computational design approach

Pierre Vandergheynst, Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Andreas Loukas, Stéphane Rosset, Andreas Scheck, Michaël Defferrard

Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted wi ...

PUBLIC LIBRARY SCIENCE2022

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

Jaume Bonet Martinez

Immune checkpoint blockade (ICB) with antibodies has shown durable clinical responses in a wide range of cancer types, but the overall response rate is still limited. Other effective therapeutic modalities to increase the ICB response rates are urgently ne ...

TAYLOR & FRANCIS INC2023

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Zander Harteveld, Fabian Sesterhenn, Stéphane Rosset, Che Yang

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

National Academy of Sciences2022

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

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck

BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...

2019

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Alisa Khramushin, Bruno Emanuel Ferreira De Sousa Correia, Patrick Daniel Barth, Jaume Bonet Martinez, Andreas Scheck, Hamed Khakzad

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and ...

NATURE PUBLISHING GROUP2020

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

Jaume Bonet Martinez

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...

OXFORD UNIV PRESS2021

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

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Fabian Sesterhenn

Vaccines have been one of the most successful interventions in global health. However, traditional vaccine development has proven insufficient to deal with pathogens that elude the immune system through highly variable and non-functional epitopes. Emerging ...

2018

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

Jaume Bonet Martinez

Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict ...

OXFORD UNIV PRESS2020

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

Bruno Emanuel Ferreira De Sousa Correia, Luciano Andres Abriata, Elisa Oricchio, Jaume Bonet Martinez, Sandrine Madeleine Suzanne Georgeon, Stéphane Rosset, Fabian Sesterhenn, Che Yang, Sabrina Susan Vollers, Elie Charles Eugène Dheilly, Patricia Corthésy Henrioud, Mélanie Evelyne Villard

De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remain ...

American Association for the Advancement of Science2020

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

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Pablo Gainza Cirauqui, Fabian Sesterhenn, Stéphane Rosset, Che Yang, Patricia Corthésy Henrioud, Sabrina Susan Vollers

Throughout the last several decades, vaccination has been key to prevent and eradicate infectious diseases. However, many pathogens (e.g., respiratory syncytial virus [RSV], influenza, dengue, and others) have resisted vaccine development efforts, largely ...

2019

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

Bruno Emanuel Ferreira De Sousa Correia, George Coukos, Jaume Bonet Martinez, Pablo Gainza Cirauqui, Sailan Shui, Sabrina Susan Vollers

The activity of CAR-T cells is reversibly halted with a small-molecule drug. Approaches to increase the activity of chimeric antigen receptor (CAR)-T cells against solid tumors may also increase the risk of toxicity and other side effects. To improve the s ...

2020

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

Bruno Emanuel Ferreira De Sousa Correia, Luciano Andres Abriata, Jaume Bonet Martinez, Sandrine Madeleine Suzanne Georgeon, Stéphane Rosset, Fabian Sesterhenn, Leo Scheller, Che Yang

De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structur ...

2021

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-alpha 7 mediated nuclear import pathway

Jaume Bonet Martinez

Influenza A viruses are able to adapt to restrictive conditions due to their high mutation rates. Importin-alpha 7 is a component of the nuclear import machinery required for avian-mammalian adaptation and replicative fitness in human cells. Here, we eluci ...

WILEY2019

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improv ...

AMER CHEMICAL SOC2021

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

Jaume Bonet Martinez

Virtually all the biological processes that occur inside or outside cells are mediated by protein-protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific ti ...

Portland Press Ltd2016

Driving Immune Responses with Synthetic Proteins - Development of De Novo Designed Immunogens to Elicit Respiratory Syncytial Virus Neutralizing Antibodies

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Stéphane Rosset, Fabian Sesterhenn, Che Yang, Patricia Corthésy Henrioud

WILEY2018

Understanding protein recognition using structural features

Jaume Bonet Martinez

Wiley-Blackwell2015