Publications related to Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Related publications (15)

Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation

While nowadays approaches for equilibrium free energy estimation are well established, nonequilibrium simulations represent both an appealing computational opportunity and a challenge. This kind of simulations allows for a trivially parallel scheme, but at ...

2025

NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual

Andrea Cavalli

Analyzing molecular surfaces to predict functional sites and identify protein cavities for small molecule binding is essential in structural biology and drug discovery, particularly when targeting allosteric sites or designing PROTACs. Moreover, measuring ...

American Chemical Society (ACS)2025

Advancements in Nanomechanical Characterization and Biomolecular Imaging with Atomic force Microscopy

Veronika Cencen

Atomic force microscopy (AFM) is a widely used imaging tool for obtaining a variety of information for a range of samples. Although it was initially intended to serve as a method of observing very flat solid surfaces, its use expanded into several other fi ...

EPFL2024

Engineered allogeneic T cells decoupling T-cell-receptor and CD3 signalling enhance the antitumour activity of bispecific antibodies

Elisa Oricchio, Marine Jeanne Françoise Bruand

Bispecific antibodies (biAbs) used in cancer immunotherapies rely on functional autologous T cells, which are often damaged and depleted in patients with haematological malignancies and in other immunocompromised patients. The adoptive transfer of allogene ...

NATURE PORTFOLIO2024

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

Maria Brbic

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 ...

Nature Publishing Group2024

Bidirectional path-based non-equilibrium simulations for binding free energy

Andrea Cavalli, Alessia Ghidini

Estimating free energy is a fundamental computational challenge, especially in complex biological systems characterised by numerous degrees of freedom. In this study, we investigate the potential of leveraging non-equilibrium free energy estimators within ...

Taylor & Francis2024

Study and optimization of the photobiomodulation effects induced on mitochondrial metabolic activity of human cardiomyocytes for different radiometric and spectral conditions

Georges Wagnières, Jaroslava Joniová, Emmanuel Louis Arthur Gerelli

Photobiomodulation (PBM) represents a promising and powerful approach for non-invasive therapeutic interventions. This emerging field of research has gained a considerable attention due to its potential for multiple disciplines, including medicine, neurosc ...

2024

Recombinant bacteria resistant to horizontal gene transfer and phage infection

Melanie Blokesch, David William Adams, Milena Jadwiga Jaskolska

The invention relates to an expression vector encoding a DNA defence system comprising polypeptides derived from Vibrio cholerae, or equivalent functional variants or homologues, conferring resistance to the maintenance of extra-genomic DNA to a recipient ...

2023

Antiviral Mechanism of Virucidal Sialic Acid Modified Cyclodextrin

Francesco Stellacci, Paulo Henrique Jacob Silva, Yong Zhu

We have reported that CD-6'SLN [6-sialyllactosamine (6'SLN)-modified beta-cyclodextrin (CD)] can be a potential anti-influenza drug because it irreversibly deactivates virions. Indeed, in vivo, CD-6'SLN improved mice survival in an H1N1 infection model eve ...

MDPI2023

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Christoph Bostedt, Camila Bacellar Cases Da Silveira

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we ...

Nature Portfolio2023

Shared metadata for data-centric materials science

Giovanni Pizzi, Gian-Marco Rignanese

The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data prin ...

Nature Portfolio2023

Human PBMCs Form Lipid Droplets in Response to Spike Proteins

Florian Maria Wurm

Intracellular lipid droplets (LDs) can accumulate in response to inflammation, metabolic stresses, and other physiological/pathological processes. Herein, we investigated whether spike proteins of SARS-CoV-2 induce LDs in human peripheral blood mononuclear ...

MDPI2023

Update on Interfacial Charge Transfer (IFTC) Processes on Films Inactivating Viruses/Bacteria under Visible Light: Mechanistic Considerations and Critical Issues

Juan Kiwi, Sami Rtimi

This review presents an update describing binary and ternary semiconductors involving interfacial charge transfer (IFCT) in composites made up by TiO2, CuO, Ag2O and Fe2O3 used in microbial disinfection (bacteria and viruses). The disinfection mechanism, k ...

2021

Unsupervised machine learning in atomistic simulations, between predictions and understanding

Michele Ceriotti

Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the final quantity of i ...

2019

Differences in viral disinfection mechanisms as revealed by quantitative transfection of Echovirus 11 genomes

Urs von Gunten, Tamar Kohn, Jason Robert Torrey

Virus inactivation mechanisms can be elucidated by methods which measure the loss of specific virus functionality (e.g., host attachment, genome internalization, genome replication). Genome functionality is frequently assessed by PCR-based methods, which a ...

2019