Many OPIGlets found their way into a DPhil in Protein Informatics through our Systems Approaches to Biomedical Sciences Industrial Doctoral Landscape Award, which was open to applicants 2009-2024. This innovative course, based at the MPLS Doctoral Training Centre (DTC), offered six months of intensive taught modules prior to starting PhD-level research, allowing students to upskill across a diverse range of subjects (coding, mathematics, structural biology, etc.) and to go on to do research in areas significantly distinct from their formal Undergraduate training. All projects also benefited from direct co-supervision from researchers working in the Pharmaceutical industry, ensuring DPhil projects in areas with drug discovery translation potential. Regrettably, having twice successfully applied for renewal of funding, we were unsuccessful in our bid to refund SABS in 2024.
Happily though, we can now formally announce that our bid for a direct successor to SABS, the Transformative Technologies in Pharmaceutical Sciences IDLA, has been backed by the BBSRC, and we will shortly be opening for applications for entry this October [2026]. As someone who benefited from the interdisciplinary training and industry-adjacency of SABS, I’m thrilled to be a co-director of this new Programme and to help deliver this course to a new generation of talented students.
At the end of September, I had the opportunity to present at the 4th Single-Domain Antibody (sdAb/VHH) Conference hosted in the city of Utrecht. The sdAb conference is a biennial event, and was held for the first time in Bonn (2019), then in Brussels (2021) and Paris (2023), before coming to the Netherlands this year.
This was the first time I’d attended a VHH-focused conference, and I was taken aback at just how large the community is; the Jaarbeurs ‘Supernova’ event hall was completely sold out, with over 400 researchers in attendance (pictures below courtesy of the organisers). The buzz reflects the ever growing interest in sdAbs as tools to discover new fundamental biology, vectors for diagnosing disease, and as prophylactic or curative therapeutics. Most every disease indication was represented at the conference, from anticancer and antiviral sdAbs to antivenom sdAbs (both for use in lateral flow tests to diagnose the snake that bit you, and as quick ‘epipen’-like therapeutics accessible even in the most remote parts of the world).
Bikes and pints across 5 pubs – what could be better (and what could go wrong). The year is 2025 and the date 06.06.25. Starting from the Stats department the customary picture was taken before the horn blown and a flood of ~30 structural biologists was unleashed onto the streets of Oxford to raid and plunder. Despite being the new kid I think Fergus will be proud to see my accurate version controlling unlike past more experienced members of the group, and that this reference doesn’t seem like copying his homework too much.
Of course even though it was June the weather was tumultuous. Having to make an educated guess on the probability of experiencing rain I took a Bayesian approach to calculate the posterior of rain occurring given the data of the entirety of British history which suggested that despite seeing sun on the BBC weather report that did not in anyway improve the likelihood of there being later rain. In light of this everyone came aptly dressed in waterproofs which turned out to be a smart choice after a later event of spontaneous beer spillage where a certain individual knocked his entire pint over Sophie and proceeded to say “at least you were wearing a raincoat”. This was a fantastic play by the newest member of the group who destroyed what little dignity (if any) he had so far amassed and simultaneously embroiled himself in the responsibility of this blog post. So to Charlotte who I know will be reading this (as I was warned!) perhaps this blog post will be an adequate first step to redemption.
And so the convoy departed towards our first stop, the Up in Arms (thanks Charlotte for the round). The inaugural table tennis tournament was held and it was great to see a real world application of the groups protein folding experience with Odysseus’s portable bike.
Next stop, the Victoria (thanks Matt for the round), before the 3.5 mile cycle to The Plough (I recommend going to the toilet before this after drinking units in the metric of pints).
Being far removed from our hunter gatherer past we settled down on the crisp summer grass with Oxford’s famous White Rabbit pizza delivered directly to the local meadow. I hadn’t grounded myself and connected to the earth like that in months (preferring to spend my days with my quadruple monitor workstation setup in the department) which combined with the beautiful settings of port meadow was making the trees look huggable. After scavenging 4 more pieces of pizza for a profit of 50% on my original contribution despite my intolerance to onions – whilst arguing that tolerance is a mental game aided by alcoholic bravery – we walked down the field to the river to reach our final destination – the idyllic medley looking over the Thames.
Reaching our last stop it dawned on me that despite proclaiming an ambitious target of 2 pints per pub I was sitting well below that at 3 pints total. It was clear desperate actions were needed to raise my average to stand up to any later scrutiny. Perhaps it was this subconscious desire to complete my self-assigned quest that at this last point of interest I executed the “swill Sophie” manoeuvre. Yet, despite my insistence that by getting through 2 pint glasses this was “technically” equivalent two my 2 pints per pub target, this did not stand up to the scrutiny of Charlotte.
After a month of wrangling with HPC molecular dynamics I’ve been getting more contact with the Slurm e-mail notification service than real human beings so it was refreshing to escape the GROMACS simulation that my brain has become and get to know the group better. Yet by the end of the night some of us (myself) couldn’t resist entering a tirade about how fractals and symmetry is the underlying representation of consciousness with the source being a strong “trust me bro”, and so it seemed liked a fitting time to put myself to bed.
The New York Times Spelling Bee is a free online word game, where players must construct as many words as possible using the letters provided in the Bee’s grid, always including the middle letter. Bonus points for using all the letters and creating a pangram.
However, this is the kind of thing which computers are very good at. If you’ve become frustrated trying to decipher the abstruse ways of the bee, let the command line help.
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.
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.
One of the nice things about OPIG, is that you can talk about something which is outside of your wheelhouse without feeling that the specialists in the group are going to eat your lunch. Last week, I gave an overview of the Hubbell group‘s Nature paper Synthetically glycosylated antigens for the antigen-specific suppression of established immune responses. I am not an immunologist by any stretch of the imagination, but sometimes you come across a piece of really interesting science and just want to say to people: Have you seen this, look at this, it’s really clever!
This blogpost is a short notice about recent quality-of-life and feature updates to our Therapeutic Structural Antibody Database (Thera-SAbDab). We hope these changes will make the database more user-friendly and facilitate new analyses…
We’ve all had things go wrong with computers, however when they go catastrophically wrong, there’s often little you can do other than to be physically on site to reinstall. This doesn’t have to be the case though. Most PCs have a tiny secondary processor which can allow full remote control of a computer that’s crashed, unresponsive or even switched off.
With the new academic year approaching, OPIG flew off to the rural paradise of Wilderhope Manor in sunny Shropshire for their annual group getaway. The goal of this retreat was assumed to be a mixture of team building, ‘conference-esque’ academic immersion, a reconnection with nature in the British countryside, and of course, a bit of fun. It is fair to say OPIG Retreat ‘23 delivered on all accounts, leaving the OPIGlets refreshed and ready for what the next year may bring.
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