Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

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In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 ...

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

The disclosure provides antibodies, or antigen-binding fragments thereof, and use thereof in prophylaxis, treatment and/or attenuation of a SARS-CoV-2 virus infection. ...

This book has been designed for instructors in higher education or adult training who wish to develop a new course or revise an existing one. It adopts a practical, visual, and modular approach based on the principle of constructive alignment. At its heart ...

Two design studios were successively taught in two schools of architecture: one at the Harvard Graduate School of Design (GSD) and the other at the Swiss Federal Institute of Technology in Lausanne (EPFL) in Lausanne, Switzerland, based on "A Global Morato ...

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

The design and discovery of potential novel materials is critical for the advancement of climate change mitigation technologies. In this respect, metal-organic frameworks (MOFs) have received considerable attention over the last two decades. The combinatio ...

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

Protein-based therapeutics, such as monoclonal antibodies and cytokines, are important therapies for various pathophysiological conditions such as oncology, autoimmune disorders, and viral infections. However, the wide application of such protein therapeut ...

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

CD4+T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on class II major histocompatibility complex (MHC-II) molecules. The high polymorphism of MHC-II genes represents an important hurdle toward ...

Vaccine technology is still facing challenges regarding some infectious diseases, which can be addressed by innovative drug delivery systems. In particular, nanoparticle-based vaccines combined with new types of adjuvants are actively explored as a platfor ...

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

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Predicting protein interactions using geometric deep learning on protein surfaces

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Opportunities and challenges in design and optimization of protein function

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Microsecond Time-Resolved Cryo-Electron Microscopy

Computational drug development for membrane protein targets

Anti-sars-cov-2 antibodies and use thereof in the treatment of sars-cov-2 infection

Course Design - A Visual and Modular Approach

Teaching Not To

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

A diversity-driven discovery of potential nanoporous materials for energy-related applications

De novo protein design by inversion of the AlphaFold structure prediction network

A new age in protein design empowered by deep learning

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

Generative power of a protein language model trained on multiple sequence alignments

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

Poloxamers Have Vaccine-Adjuvant Properties by Increasing Dissemination of Particulate Antigen at Distant Lymph Nodes