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

Publications associées (40)

Inherent Structural Descriptors Via Machine Learning

Finding proper collective variables for complex systems and processes is one of the most challenging tasks in simulations, which limits the interpretation of experimental and simulated data and the application of enhanced sampling techniques. Here, we prop ...

IOP Publishing Ltd2025

Programming Light Propagation for Efficient Artificial Intelligence

Ilker Oguz

Contemporary artificial intelligence (AI) models' exponentially growing complexity translates to their expanding skill sets. They can create language or image content mimicking human creativity and understanding, becoming indispensable tools in education, ...

EPFL2025

Scaling the Modalities in Multimodal Foundation Models

Oguzhan Fatih Kar

Having a single neural network to handle a wide and varied range of tasks and modalities has been a long-standing goal. Such a model brings notable advantages, such as test-time computational efficiency, modality fusion, and reduced model size. Our goal in ...

EPFL2025

Bayes-optimal learning of deep random networks of extensive-width*

Lenka Zdeborová, Florent Gérard Krzakala, Hugo Chao Cui

We consider the problem of learning a target function corresponding to a deep, extensive-width, non-linear neural network with random Gaussian weights. We consider the asymptotic limit where the number of samples, the input dimension and the network width ...

IOP Publishing Ltd2025

LIU-NET: lightweight Inception U-Net for efficient brain tumor segmentation from multimodal 3D MRI images

Zaffar Ahmed Shaikh

Segmenting brain tumors is a critical task in medical imaging that relies on advanced deep-learning methods. However, effectively handling complex tumor regions requires more comprehensive and advanced strategies to overcome challenges such as computationa ...

2025

Data-driven dynamic friction models based on Recurrent Neural Networks

Gaëtan Bixente Cortes, Antonio Joaquin Garcia Suarez

In this concise contribution, it is demonstrated that Recurrent Neural Networks (RNNs) based on Gated Recurrent Unit (GRU) architecture, possess the capability to learn the complex dynamics of rate-and-state friction (RSF) laws from synthetic data. The dat ...

2025

From Preprocessing to Evaluation: The Role of External Knowledge in Advancing Language Models and Machine Translation

Georgios Vernikos

Machine translation (MT) systems and language models (LMs) have demonstrated impressive performance in recent years, driven by advances in architecture, algorithms, and the scaling of parameters and training data. Despite the ability of these models to int ...

EPFL2025

Optical Processors for AI Computing and Networking

Mustafa Yildirim

Computing has long been central to technological advancements, where each leap in compute power has catalyzed applications once thought impossible, such as smartphones. Recently, the exponential growth in the compute demand of artificial intelligence (AI) ...

EPFL2025

Deep learning for enhancement of low-resolution and noisy scanning probe microscopy images

Georg Fantner, Marcos Penedo Garcia

In this study, we employed traditional methods and deep learning models to improve resolution and quality of low-resolution AFM images made under standard ambient scanning. Both traditional methods and deep learning models were benchmarked and quantified r ...

Beilstein Institut2025

Towards Integrated Processing of Physiological Signals and Speech

Zohreh Mostaani

Research in speech processing has largely focused on source-system modeling, where vocal fold vibrations serve as the source and the vocal cavity's articulations as the system. Nonetheless, speech production includes a complex combination of physiological ...

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

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

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

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

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

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

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

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

Machine learning-aided generative molecular design

Philippe Schwaller, Jeff Guo

Machine learning has provided a means to accelerate early-stage drug discovery by combining molecule generation and filtering steps in a single architecture that leverages the experience and design preferences of medicinal chemists. However, designing mach ...

Nature Portfolio2024