Publication
Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design
Publications associées (38)
Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications
Evolution has created, selected and evolved large repertoires of proteins that operate in various biological systems. Nowadays biotechnological needs are coming up orders of magnitude faster than proteins naturally evolve. The emergence of de novo protein ...
EPFL2020Inter-laboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry
Yury Tsybin, Natalia Gasilova, Laure Menin, Luca Fornelli, Kristina Srzentic
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary s ...
2020De novo protein design enables the precise induction of RSV-neutralizing antibodies
Luciano Andres Abriata, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Sandrine Madeleine Suzanne Georgeon, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang, Patricia Corthésy Henrioud, Sabrina Susan Vollers, Elie Charles Eugène Dheilly, Mélanie Evelyne Villard, Yujia Wang
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 ...
2020Expanding beyond the natural protein repertoire to engineer targeted vaccines and diagnostics
Proteins have evolved over millions of years to carry out the vast majority of biological functions that are fundamental to life. Their three-dimensional structures and functions have been in the focus of biomedical research for many decades, and substanti ...
EPFL2019Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank
Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti
Rationalizing the structure and structure–property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as buildin ...
2019A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments
Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo
We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of mode ...
WILEY2019Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Pablo Gainza Cirauqui, Freyr Sverrisson
Predicting interactions between proteins and other biomolecules solely based on structure remains a challenge in biology. A high-level representation of protein structure, the molecular surface, displays patterns of chemical and geometric features that fin ...
2019Introducing tolerance to foreign and partly foreign proteins by erythrocyte binding and artificial glycosylations
Over the last few years, protein drugs have steadily gained importance in the clinic. Compared to small molecule drugs, protein drugs are taken up by antigen presenting cells, which degrade the proteins into peptides that are then presented on major histoc ...
EPFL2018An Automatic, Data-Driven Definition of Atomic-Scale Structural Motifs
Structure-property relationships at the atomic scale are usually understood in terms of recurrent structural motifs formed by atoms and molecules, and how they transform and interact with each other.
We introduce with this thesis a novel analysis approach, ...
EPFL2018Mid-Infrared plasmonic nanoantennas for ultrasensitive detection of proteins and their secondary structure
Engineered plasmonic nanostructures have emerged as powerful sensing platforms and are promoting novel applications in various fields. By providing extreme field confinement down to molecular dimensions and enhancing light-matter interaction at the nanosca ...
EPFL2018