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

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High-dimensional data must be highly structured to be learnable. Although the compositional and hierarchical nature of data is often put forward to explain learnability, quantitative measurements establishing these properties are scarce. Likewise, accessin ...

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 ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

This dataset contains a collection of ultrafast ultrasound acquisitions from nine volunteers and the CIRS 054G phantom. For a comprehensive understanding of the dataset, please refer to the paper: Viñals, R.; Thiran, J.-P. A KL Divergence-Based Loss for In ...

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 ...

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 ...

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 ...

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 ...

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

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 ...

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 ...

Epilepsy, a major neurological disease, requires careful diagnosis and treatment. However, the detection of epileptic seizures remains a significant challenge. Current clinical practice relies on expert analysis of EEG signals, a process that is time-consu ...

Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and ...

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

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

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Probing the latent hierarchical structure of data via diffusion models

Recording physiological history of cells with chemical labeling

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (2/6)

Predicting protein interactions using geometric deep learning on protein surfaces

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (3/6)

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

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (4/6)

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

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (5/6)

A KL Divergence-Based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (6/6)

Opportunities and challenges in design and optimization of protein function

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Microsecond Time-Resolved Cryo-Electron Microscopy

Computational drug development for membrane protein targets

Resource-Efficient Continual Learning for Personalized Online Seizure Detection

A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins

Mechanisms and functions of protein S-acylation

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli