Structural Biology seminars

This webinar uses research on Chagas disease to explain how predicted protein structures can support drug discovery when experimental structures are unavailable. In the example study, AlphaFold models of Trypanosoma cruzi proteins supported a virtual screen of roughly 30,000 compounds; subsequent experiments identified antiparasitic activity in two approved drugs. The session introduces AlphaFold confidence measures and ways to obtain models, then follows a screening workflow through binding-pocket prediction, chemical-library selection, docking, and interpretation of results. It discusses difficulties encountered when docking against predicted structures and considerations for adapting the workflow to other targets. The material is intended for doctoral students, early-career researchers, and other drug-discovery professionals.

Jan Kosinski explains how AlphaFold-style methods predict protein complexes and why their reliance on evolutionary information makes interactions between host and pathogen proteins especially difficult. The talk reviews large-scale studies, interpreting both successful predictions and failures rather than treating reported success rates as universal performance. It then examines ways to improve predictions through broader sampling, altered sequence alignments and experimental restraints, including crosslinking mass spectrometry, with influenza A virus as a worked research example. The session is suitable for students and researchers interested in host-pathogen interactions and structural bioinformatics; basic knowledge of protein structures and sequence alignments is useful, but prior AlphaFold experience is unnecessary.

Ilaria Ferlenghi discusses a career spanning structural biology, cryo-electron microscopy, vaccine research and development, and the growing role of artificial intelligence and machine learning in scientific innovation and entrepreneurship.

Parasites persist despite continual exposure to immune molecules and cells. African trypanosomes live in serum and tissues, while intracellular parasites such as malaria parasites display their own proteins on host cells. This seminar examines how parasites avoid detection and clearance through antigenic variation and surface proteins that suppress immune cells or their effectors. It also considers the experimental and computational approaches used to investigate these mechanisms, showing the diversity of adaptations that permit parasites to resist immunity. The presentation is intended for students and researchers interested in infection, immunity and evolution; undergraduate biology is helpful.

In situ cryo-electron tomography can reveal interactions between pathogens and their hosts inside intact cellular environments. This seminar uses apicomplexan parasites and gram-negative bacteria to explain the workflow from sample preparation through image acquisition and analysis. It covers freezing, cryo-focused ion beam milling, cryo-electron tomography, correlative light and electron microscopy, tomogram reconstruction, segmentation and subtomogram averaging. The presentation discusses which aspects of the host-pathogen interface these approaches can resolve, their advantages and limitations, and when they suit a research question. Familiarity with the organisms or cryo-electron microscopy is helpful but not required.

Infection research is identifying molecular targets involved in pathogen replication, metabolism and essential host functions, but translating discoveries into treatments requires functional validation. Advances in X-ray crystallography now permit larger-scale screening of fragments and other small molecules against these targets. This seminar presents technologies developed at EMBL Grenoble for fully automated fragment and ligand screening, and their use in investigating infection-related targets with therapeutic potential. It connects structural screening with small-molecule inhibitor development, target validation and evidence for therapeutic feasibility. The session is relevant to infection biology, chemical biology, structural biology and drug discovery.

José Molina Mora presents an integrative study of the core stress-response mechanisms, or perturbome, of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Transcriptomic data are analysed using machine learning, systems biology, functional enrichment and ortholog comparisons to prioritise stress-associated genes. Experimentally determined protein structures are combined with AlphaFold predictions where structural data are missing. Molecular docking and further computational analyses then identify preliminary compounds and conditions that might inhibit selected targets. These results are a proof of concept awaiting experimental validation. The talk connects gene-expression analysis with structural modelling for antimicrobial research and is aimed at researchers, graduate students and professionals in microbiology, bioinformatics and related biomedical fields.

This webinar explores computational and structure-based vaccine design, comparing prefusion stabilisation of vaccine antigens with epitope scaffolding onto non-antigen protein backbones. It discusses the advantages and limitations of both strategies. No background in computational protein design is required; familiarity with vaccine antigens and viral glycoproteins is helpful. Free online webinar; advance registration and details: https://www.ebi.ac.uk/training/events/strategies-computational-vaccine-design-prefusion-stabilisation-epitope-focussing/

Open biological data resources connect complementary evidence about proteins involved in infection. Using influenza haemagglutinin, this seminar demonstrates sequence and functional annotations in UniProt, three-dimensional cryo-EM maps in EMDB, and experimental and predicted structures in PDBe and the AlphaFold Protein Structure Database. Participants will learn to browse, retrieve and interpret these data and follow connections between the resources. The session also considers how accessible biological data supports infection research and pandemic preparedness. It is aimed at students and researchers in protein biology, structural biology and bioinformatics; basic knowledge of sequence and structure formats is useful.