Publications associées à Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Publications associées (37)

Sequential Reasoning with Socially Caused Beliefs

Machine learning and artificial intelligence methods have achieved remarkable success, matching and even surpassing human capabilities in various complex tasks. However, many demonstrations have generally neglected a critical part of the intelligence that ...

EPFL2025

The effect of hydration and dynamics on the mass density of single proteins

Lucas Sebastian Powell-Rudden

The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses molecular dynamics sim ...

2025

Computational design of complex protein folds and soluble analogs of membrane proteins

Casper Alexander Goverde

Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

EPFL2025

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

Zhidian Zhang

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 ...

EPFL2024

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

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 ...

EPFL2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

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 ...

Nature Portfolio2024

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

Anthony Marchand

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 ...

EPFL2024

Recording physiological history of cells with chemical labeling

Kai Johnsson, Julien Hiblot

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

American Association for the Advancement of Science2024

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

Mahdi Hijazi

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 ...

EPFL2024

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

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

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

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 ...

eLIFE SCIENCES PUBL LTD2023

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

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 ...

EPFL2024

Characterising directed and undirected metrics of high-order interdependence

Michael Christoph Gastpar

Systems of interest for theoretical or experimental work often exhibit high-order interactions, corresponding to statistical interdependencies in groups of variables that cannot be reduced to dependencies in subsets of them. While still under active develo ...

Institute of Electrical and Electronics Engineers Inc.2024

A new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Casper Alexander Goverde, Arne Schneuing, Hamed Khakzad, Ilia Igashov

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 ...

Cell Press2023

Computational drug development for membrane protein targets

Pierre Vogel, Henning Paul-Julius Stahlberg, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

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 ...

2024

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

Benedict Dieter Gregor Wolf, Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Hamed Khakzad

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 ...

2023

Informed Graph Learning By Domain Knowledge Injection and Smooth Graph Signal Representation

Olga Fink, Lukas Kühn, Gaëtan Michel Frusque, Keivan Faghih Niresi

Graph signal processing represents an important advancement in the field of data analysis, extending conventional signal processing methodologies to complex networks and thereby facilitating the exploration of informative patterns and structures across var ...

IEEE2024

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Pablo Gainza Cirauqui, Michael Bronstein, Zander Harteveld, Andreas Scheck, Sarah Wehrle, Anthony Marchand, Alexandra Krina Van Hall-Beauvais, Freyr Sverrisson

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023