Category Archives: Antibodies

Handling OAS Scale Datasets Without The Drama

Working with Observed Antibody Space (OAS) dataset sometimes feels a bit like trying to cook dinner with the contents of the whole fridge emptied into the pan. There are countless CSVs, all of different sizes (some might not even fit onto your RAM), and you just want a clean, fast pipeline so you can get back to modelling. The trick is to stop treating the data like a giant spreadsheet you fully load into memory and start treating it like a columnar, on-disk database you stream through. That’s exactly what the 🤗 Datasets library gives you.

At the heart of 🤗 Datasets is Apache Arrow, which stores columns in a memory-mapped format (if you are curious about what that means there is a great explanation in another blog post here. In plain terms: the data mostly lives on disk, and you pull in just the slices you need. It feels interactive even when the dataset is huge. Instead of a single monolithic script that does everything (and takes forever), you layer small, composable steps—standardize a few columns, filter out junk, compute a couple of derived fields—and each step is cached automatically. Change one piece, and only that piece recomputes. Sounds great, right? But of course, the key question now is how to get OAS data into Datasets to begin with.

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Antibody developability datasets

Next to binding the antigen with high affinity, antibodies for therapeutic purposes need to be developable. These developability properties includes high expression, high stability, low aggregation, low immunogenicity, and low non-specificity [1]. These properties are often linked and therefore optimising for one property might be at the expense of another. Machine learning methods have been build to guide the optimistation process of one or multiple developability properties.

Performance of these methods is often limited by the amount and type of data available for training. These dataset contain experimental determined scores of biophysical assays related to developability. Some common experimental assays are described in a previous blog post by Matthew Raybould [2]. Here I will discuss some (commonly) used and new dataset related to antibody developability. This list is not exhaustive but might help you start understanding more about antibody developability.

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A Masterclass in Basic & Translational Immunology with Prof. Abul Abbas

On Thursday 17th April, a group of us made the journey ‘up the hill’ to the Richard Doll building to attend an immunology masterclass from Professor Abul Abbas. Prof. Abbas is an emeritus professor in Pathology at UCSF and author of numerous core textbooks including Basic Immunology: Functions and Disorders of the Immune System.

The whole-day course consisted of a series of lectures covering core topics in immunology, from innate immunity and antigen presentation through to B/T cell subsets, autoimmunity, and immunotherapy.

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Therapeutic antibodies and their function

Last week during a poster session in the Department of Statistics, I had an interesting discussing with Martin Buttenschoen (working on the other side of the group) regarding the difference between small molecules and antibodies as therapeutics. This discussion made me realise that even though I’m working on antibodies engineering and developability, I could use a little refresher on approved therapeutic antibodies and their mechanisms of action. 

In case you also need this bigger picture, or want to get excited about therapeutic antibodies yourself, I will summarise the target, the development process, the molecular function, and the administration for three successful therapeutic antibodies.

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The “AI-ntibody” Competition: benchmarking in silico antibody screening/design

We recently contributed to a communication in Nature Biotechnology detailing an upcoming competition coordinated by Specifica to evaluate the relative performance of in vitro display and in silico methods at identifying target-specific antibody binders and performing downstream antibody candidate optimisation.

Following in the footsteps of tournaments such as the Critical Assessment of Structure Prediction (CASP), which have led to substantial breakthroughs in computational methods for biomolecular structure prediction, the AI-ntibody initiative seeks to establish a periodic benchmarking exercise for in silico antibody discovery/design methods. It should help to identify the most significant breakthroughs in the space and orient future methods’ development.

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The wider applications of nanobodies

This week, it was my turn to give the short talk at our group meeting. I chose to present a recently published paper on thermostability prediction for nanobodies. The motivation for this work, at least in part, is the need for thermostability in the diverse applications of nanobodies. At OPIG, our research primarily revolves around the therapeutic uses of nanobodies, but their potential extends beyond this. I thought it would be interesting to highlight some of these broader applications here:

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Conference summary: Generative AI in Life Science

This year I attended the second edition of Generative AI in Life Science (GenLife – https://genlife.dk/) and it was an enriching experience that I thoroughly enjoyed. Held in Copenhagen, the event brought together researchers from different areas of AI applied to the life sciences and provided a fantastic platform for networking, learning and sharing ideas. The programme included a mix of long and short talks from experts in the field, but also had a significant presence of emerging PIs, making the conference a perfect place to discover emerging groups in the field. Here I have collected some highlights of the talks I have enjoyed the most at the conference.

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Conference Summary: MGMS Adaptive Immune Receptors Meeting 2024

On 5th April 2024, over 60 researchers braved the train strikes and gusty weather to gather at Lady Margaret Hall in Oxford and engage in a day full of scientific talks, posters and discussions on the topic of adaptive immune receptor (AIR) analysis!

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