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Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

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Deep learning approaches for conformational flexibility and switching properties in protein design

Patrick Daniel Barth, Mahdi Hijazi

Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...

2022

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Sarah Wehrle

Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...

EPFL2022

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Protein–protein interactions (PPIs) govern numerous cellular functions in terms of signaling, transport, defense and many others. Designing novel PPIs poses a fundamental challenge to our understanding of molecular interactions. The capability to robustly ...

2022

Biological nanopores for single-molecule sensing

Matteo Dal Peraro, Chan Cao, Simon Finn Mayer

Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and ou ...

2022

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current st ...

SWISS CHEMICAL SOC2022

On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C

Andreas Scheck

Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...

EPFL2021

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 ...

BMC2021

Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...

IEEE COMPUTER SOC2021

Computational design of highly signaling active membrane receptors through de novo solvent-mediated allosteric networks

Jian Wang, Patrick Daniel Barth

Protein catalysis and allostery require the atomic-level orchestration and motion of residues, ligand, solvent and protein effector molecules, but the ability to design protein activity through precise protein-solvent cooperative interactions has not been ...

2021

An Oculus to Profile and Probe Target Engagement In Vivo: How T-REX Was Born and Its Evolution into G-REX

Yimon Aye, Chloé Rogg

Here we provide a personal account of innovation and design principles underpinning a method to interrogate precision electrophile signaling that has come to be known as "REX technologies". This Account is framed in the context of trying to improve methods ...

AMER CHEMICAL SOC2021