Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins

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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 ...

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 ...

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 ...

Effective Prognostics and Health Management (PHM) relies on accurate prediction of the Remaining Useful Life (RUL). Data-driven RUL prediction techniques rely heavily on the representativeness of the available time-to-failure trajectories. Therefore, these ...

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 ...

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 ...

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 ...

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 ...

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 ...

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, ...

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 ...

β-lactamases from Gram-negative bacteria are generally regarded as soluble, periplasmic enzymes. NDMs have been exceptionally characterized as lipoproteins anchored to the outer membrane. A bioinformatics study on all sequenced beta-lactamases was performe ...

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

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 ...

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 ...

The prospect of massive parallelism of optics enabling fast and low energy cost operations is attracting interest for novel photonic circuits where 3-dimensional (3D) implementations have a high potential for scalability. Since the technology for data inpu ...

One of the barriers to further commercialization of the proton exchange membrane fuel cell (PEMFC) is hydrogen storage. Conventional methods are based on pressurizing the hydrogen up to 700 bar. The focus of this study is to characterize the hydrogen stora ...

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 ...

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 ...

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 ...

Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins

Chattez avec Graph Search

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

Predicting protein interactions using geometric deep learning on protein surfaces

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

Domain adaptation via alignment of operation profile for Remaining Useful Lifetime prediction

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

Opportunities and challenges in design and optimization of protein function

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

Recording physiological history of cells with chemical labeling

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

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

Mechanisms and functions of protein S-acylation

OXA β-lactamases from Acinetobacter spp. are membrane bound and secreted into outer membrane vesicles

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

A new age in protein design empowered by deep learning

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

From 3D to 2D and back again

Simulation and optimization of the impacts of metal-organic frameworks on the hydrogen adsorption using computational fluid dynamics and artificial neural networks

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

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis