EMBL-EBI

Bacteriophage genomes offer a large reservoir of enzymes adapted to extreme environments. This seminar examines endolysins, enzymes that break down bacterial cell walls, as potential antimicrobial agents for agriculture, food production and sanitation. Cold-adapted variants could support cleaning at lower temperatures, while heat-tolerant variants may serve fermentation, food processing and alternatives to antibiotics. Amy Wiseman presents research combining metagenomic sequences from Icelandic hot springs and Arctic seawater with AlphaFold and other prediction methods, biophysical experiments, X-ray crystallography and biochemical characterization. The work investigates candidate cold-adapted and thermophilic endolysins, reveals unexpected structural features, and considers what these features imply for evolution, environmental adaptation and enzyme function. The talk connects sequence mining and structural prediction with experimental validation, biotechnology applications and rational enzyme design.

Interpreting human missense variants requires connecting genomic coordinates with protein sequences, structures and functional evidence. ProtVar integrates annotations and predictions from UniProt, Ensembl, PDBe, Open Targets and AlphaFoldDB, extending variant lookup to discovery across more than 500 million potential missense variants. This seminar demonstrates natural-language searches using diseases, pathways and drug responses, multi-criteria filtering, structural visualisation and data export. Participants will learn to prioritise variants, interpret their structural and functional effects, and retrieve data through web downloads or the REST API. The session serves geneticists, drug-discovery researchers and computational biologists; undergraduate molecular biology and genetics are recommended.

Protein-structure prediction can help distinguish competing gene models. Studies of two fungi and an apicoplast compare original and manually curated annotations, finding that structure-derived scores favour curated models when predictions differ in structured domains. These signals complement sequence-domain analysis but offer little help for uncertainty in potentially disordered regions. The presentation also examines Protenix-mini as a faster alternative retaining discriminatory power, complete-proteome scoring, and a NextFlow pipeline intended to make the workflow usable. It considers applications when transcriptomic evidence is limited and the remaining limitations of structure-based annotation.

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.

MGnify supports microbiome research through versioned pipelines for taxonomic and functional analysis and access to previously analysed public and submitted datasets. This introduction explains the resource’s data types—amplicons, raw reads, assemblies, genomes and proteins—and how studies, samples and sequencing runs connect to analyses, visualisations and downloadable results. It covers browsing and programmatic access for further exploration and introduces the subsequent metagenomics webinar series. The session is intended for life-science students and researchers; familiarity with DNA sequencing helps, while specialist coding or bioinformatics experience is unnecessary.

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/

Laboratory-evolved gentamicin-resistant bacteria are analysed using whole-genome sequencing and protein-structure modelling. The study focuses on mutations in elongation factor G and compares AlphaFold2 predictions with wild-type proteins. Aligning predicted EF-G structures with experimental ribosome and antibiotic-bound structures reveals how local conformational and physicochemical changes could affect drug binding. The talk examines subtle structural shifts, mutations without detectable structural changes, and the limitations of prediction alone. It presents a workflow that combines genomic evidence, AI models and experimental structures to form mechanistic hypotheses about antimicrobial resistance.

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.

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.

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.

This webinar explains how researchers can retrieve and analyse protein information using UniProt. It demonstrates advanced queries, BLAST searches, peptide searches, and multiple-sequence alignments, including how to navigate outputs and use functional annotations to interpret them. It also discusses how identifiers, ontologies, and controlled vocabularies organize biological knowledge, and how identifier mapping connects resources. The session is suitable for scientists at any career stage who want to use UniProt or extend their existing skills; undergraduate-level biology knowledge is helpful.

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.

Scientific computing has environmental impacts that extend beyond the growing use of artificial intelligence. This seminar examines how research computing affects the environment, how researchers can measure and reduce those effects, and how funders are responding. It also asks whether efficiency alone provides an adequate strategy. The speakers introduce Green DiSC, a certification scheme for sustainable computing, and the Environmentally Sustainable Computational Science community forum. The discussion connects practical choices in computational research with community approaches to sustainability and concludes with questions. It is suitable for researchers and software developers without prior knowledge of sustainable computing.

This webinar examines reconstruction and use of marine metagenome-assembled genomes. The first part introduces the Ocean Microbiomics Database as a standardized resource for prokaryotic genome-resolved analysis, including co-abundance-based reconstruction, contextual metadata, and relationships between ecological patterns and microbial genomes. The second part considers why eukaryotic genomes are harder to recover: their complexity, low abundance, and limited markers and reference sequences complicate assembly and classification. Participants will compare reconstruction approaches, explore the database, and consider tools and steps for recovering eukaryotic genomes. The session serves academic and industrial researchers developing marine-microbiome applications and infrastructure teams managing samples, data, and discovery resources.

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.

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.