Publications related to A new age in protein design empowered by deep learning

Related publications (37)

Does surface completion fail to support uncrowding?

In crowding, perception of a target deteriorates in the presence of nearby elements. As the entire stimulus configuration across large parts of the visual field influences crowding and not just nearby elements, low-level explanations, such as local pooling ...

Association for Research in Vision and Ophthalmology (ARVO)2025

Uncovering neural architectures enabling robust and flexible motor control in Drosophila

Femke Imreh Hurtak

Uncovering the neural architectures that enable robust and flexible motor control is a fundamental challenge in neuroscience. Understanding the neural circuitry organisation at a cellular level is crucial for advancing our knowledge and developing interven ...

EPFL2025

Efficient Direct Cytosolic Protein Delivery via Protein-Linker Co-engineering

Colleen Noel Loynachan, Francesco Stellacci, Lixia Wei, Heyun Wang, Suiyang Liao, Melis Özkan

Protein therapeutics have enormous potential for transforming the treatment of intracellular cell disorders, such as genetic disorders and cancers. Due to proteins’ cell-membrane impermeability, protein-based drugs against intracellular targets require eff ...

American Chemical Society (ACS)2025

Enhancing Multifunctional Drug Screening via Artificial Intelligence

Horst Arthur Vogel

Computational drug screening is of fundamental importance in early-stage drug discovery. The current computational methods predict compound affinities to their targets based on docking or pharmacophore (PH4) hypotheses. Here, we develop Alpha-Pharm3D, a ve ...

ROYAL SOC CHEMISTRY2025

Artificial Metalloenzymes with Multiple Catalytic Sites for Tandem or Synergistic Transformations

Weijin Wang

Artificial metalloenzymes (ArMs) combine the broad reactivity of transition metals with the exquisite selectivity of enzymes, expanding the scope of biocatalysis beyond natural enzymatic functions. The biotin-streptavidin (Sav) system offers a versatile sc ...

EPFL2025

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

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

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

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

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

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, ...

PMLR2024

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

Deep learning approach for identification of H II regions during reionization in 21-cm observations - II. Foreground contamination

Jean-Paul Richard Kneib, Emma Elizabeth Tolley, Michele Bianco, Tianyue Chen

The upcoming Square Kilometre Array Observatory will produce images of neutral hydrogen distribution during the epoch of reionization by observing the corresponding 21-cm signal. However, the 21-cm signal will be subject to instrumental limitations such as ...

Oxford Univ Press2024

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

Safe Deep Neural Networks

Kyle Michael Matoba

The capabilities of deep learning systems have advanced much faster than our ability to understand them. Whilst the gains from deep neural networks (DNNs) are significant, they are accompanied by a growing risk and gravity of a bad outcome. This is troubli ...

EPFL2024

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

Deep Learning Theory Through the Lens of Diagonal Linear Networks

Scott William Pesme

In this PhD manuscript, we explore optimisation phenomena which occur in complex neural networks through the lens of

2

-layer diagonal linear networks. This rudimentary architecture, which consists of a two layer feedforward linear network with a diagonal ...

EPFL2024

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

Infusing structured knowledge priors in neural models for sample-efficient symbolic reasoning

Mattia Atzeni

The ability to reason, plan and solve highly abstract problems is a hallmark of human intelligence. Recent advancements in artificial intelligence, propelled by deep neural networks, have revolutionized disciplines like computer vision and natural language ...

EPFL2024

Performing and Detecting Backdoor Attacks on Face Recognition Algorithms

Alexander Carl Unnervik

The field of biometrics, and especially face recognition, has seen a wide-spread adoption the last few years, from access control on personal devices such as phones and laptops, to automated border controls such as in airports. The stakes are increasingly ...

EPFL2024

Reduced Training Data for Laser Ultrasound Signal Interpretation by Neural Networks

Romain Christophe Rémy Fleury, Janez Rus

The performance of machine learning algorithms is conditioned by the availability of training datasets, which is especially true for the field of nondestructive evaluation. Here we propose one reconfigurable specimen instead of numerous reference specimens ...

2024

Task-driven neural network models predict neural dynamics of proprioception: Neural network model weights

Alexander Mathis, Alberto Silvio Chiappa, Alessandro Marin Vargas, Axel Bisi

Proprioception tells the brain the state of the body based on distributed sensors in the body. However, the principles that govern proprioceptive processing from those distributed sensors are poorly understood. Here, we employ a task-driven neural network ...

Zenodo2024