From transcriptomics to structural modeling with AlphaFold: analysis of the central response to stress in bacteria using machine learning and structural bioinformatics

In this webinar, we will present our research focused on understanding the core mechanisms (perturbome) employed by prokaryotic organisms to survive and adapt to diverse stress conditions. Our analyses are based on transcriptomic datasets from the bacterial models Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, in which gene expression analyses and the prioritization of stress-response-associated genes were performed using machine learning, systems biology, functional enrichment, and orthologous analyses.

Subsequently, we implemented structural bioinformatics approaches integrating experimentally resolved protein structures available in PDB and AlphaFold-based predictions for proteins lacking experimental structural data. Using these protein structures, molecular docking and other in silico analyses enabled the identification of a preliminary set of compounds and potential conditions capable of inhibiting these molecular targets as a proof of concept. Future experimental validation studies are expected to confirm the computational findings obtained through this integrative framework.

This event is part of a broader webinar series on user cases of the AlphaFold resources. For more information about the series and its webinars, please visit the following link: AlphaFold in practice: research use cases | EMBL-EBI Training

Who is this course for?

This webinar is intended for researchers, graduate students, and professionals in microbiology, bioinformatics, computational biology, and related biomedical sciences interested in the use of AlphaFold for protein structure prediction and its integration with omic sciences, bioinformatics, systems biology, molecular docking, and in silico antimicrobial target discovery approaches.

Outcomes

By the end of the webinar, you will be able to:

• Understand the application of bioinformatics approaches for the analysis of bacterial stress-response proteins and the analysis of core perturbomes.
• Recognize the integration of transcriptomics, machine learning, structural modeling, and AlphaFold for the identification of potential molecular targets.
• Describe the use of experimentally resolved structures from PDB and AlphaFold-predicted models in downstream structural analyses.
• Appreciate the potential of integrative computational frameworks combining omics and structural bioinformatics for future antimicrobial research.

This webinar, hosted on Zoom Webinar, is free to attend, but you need to register for a place beforehand, using the 'Register' button. Once registered, you will receive a confirmation email with a link to join the webinar.

The webinar will be recorded, and the recording will be made available on this page one day after the event. Please note that we do not issue certificates of attendance for our webinars. However, you will receive an email from our Zoom account confirming your participation a day after the event