New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

Chat with Graph Search

Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.

DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.

Solid-state nanopores offer the possibility of detecting disease biomarkers in early diagnostic applications. Standard approaches harness fingerprinting, where protein targets are bound to DNA carriers and detected in free translocation with a solid-state ...

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 synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Heterostructures consisting of SmNiO3 and NdNiO3 alternating layers with additional LaAlO3 spacer layers were grown and fully characterized by means of x-ray diffraction, atomic force microscopy, and scanning transmission electron microscopy. A change in t ...

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 invention of 3D atomic force microscopy (3D-AFM) has enabled visualizing subnanoscale 3D hydration structures. Meanwhile, its applications to imaging flexible molecular chains have started to be experimentally explored. However, the validity and princi ...

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, ...

Living photovoltaics are microbial electrochemical devices that use whole cell–electrode interactions to convert solar energy to electricity. The bottleneck in these technologies is the limited electron transfer between the microbe and the electrode surfac ...

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 ...

Preventing the misfolding or aggregation of TDP-43 is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. In our work, we provide proof of concept that native state stabili ...

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 ...

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 ...

Control of nanomaterial dimensions with atomic precision through synthetic methods is essential to understanding and engineering of nanomaterials. For single-layer inorganic materials, size and shape controls have been achieved by self-assembly and surface ...

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

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 ...

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 tension–tension fatigue behavior of pseudo-ductile hybrid bonded-bolted double lap basalt composite joints, composed of pseudo-ductile adhesives and adherends with multi-directional fiber architecture, was experimentally investigated. The fatigue damag ...

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 ...

Intravenous (IV) iron-carbohydrate complexes are widely used nanoparticles (NPs) to treat iron deficiency anaemia, often associated with medical conditions such as chronic kidney disease, heart failure and various inflammatory conditions. Even though a ple ...

This paper presents a novel hybrid framework for generating and updating a synthetic population. We call it hybrid because it combines model-based and data-driven approaches. Existing generators produce a snapshot of synthetic data that becomes outdated ov ...

New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

Chat with Graph Search

Controlled Sensing of User-Defined Aptamer-Based Targets Using Scanning Ionic Conductance Spectroscopy

Microsecond Time-Resolved Cryo-Electron Microscopy

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Structural study of nickelate based heterostructures

Predicting protein interactions using geometric deep learning on protein surfaces

Revealing the Mechanism Underlying 3D-AFM Imaging of Suspended Structures by Experiments and Simulations

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

Polydopamine-coated photoautotrophic bacteria for improving extracellular electron transfer in living photovoltaics

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

Targeting TDP-43 Proteinopathies in Neurodegeneration by its Native-State Stabilization

Opportunities and challenges in design and optimization of protein function

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

Controlled Formation of Nanoribbons and Their Heterostructures via Assembly of Mass-Selected Inorganic Ions

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

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

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

Tension-tension fatigue behavior of basalt composite hybrid joints

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

Iron-carbohydrate complexes treating iron anaemia: Understanding the nano-structure and interactions with proteins through orthogonal characterisation

Hybrid Simulator for Capturing Dynamics of Synthetic Populations