Publication
Bicyclic peptide ligands pulled out of cysteine-rich peptide libraries
Publications associées (32)
Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection
Nako Nakatsuka, Xinyu Zhang, Haiying Hu
Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale pr ...
2024Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design
Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...
EPFL2024From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors
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 ...
EPFL2024Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis
Patrick Daniel Barth, Robert Everett Jefferson
The present invention relates to a computer-implemented method for engineering the interaction between a protein and a cognate peptide that are capable of forming a molecular complex, wherein the method comprises (a) preparing in silico a library of test p ...
2023A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
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 ...
EPFL2023Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions
The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...
EPFL2022Computational design of novel protein–protein interactions – An overview on methodological approaches and applications
Bruno Emanuel Ferreira De Sousa Correia, Anthony Marchand, Alexandra Krina Van Hall-Beauvais
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 ...
2022Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors
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 ...
EPFL2022On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C
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 ...
EPFL2021Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning
The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...
EPFL2021