In our latest immunoinformatics review, OPIG has teamed up with experienced antibody consultant Dr. Anthony Rees to outline the evidence for BCR/antibody repertoire convergence on common epitopes post-pathogen exposure, and all the ways we can go about detecting it from repertoire gene sequencing data. We highlight the new advances in the repertoire functional analysis field, including the role for OPIG’s latest tools for structure-aware antibody analytics: Structural Annotation of AntiBody repertoires+ (SAAB+), Paratyping, Ab-Ligity, Repertoire Structural Profiling & Structural Profiling of Antibodies to Cluster by Epitope (‘SPACE’).
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An A-Z of Oxford
The 2021/2 academic year is now well underway in Oxford, which means a fresh batch of new students getting to grips with some of the bewildering terminology employed here, as well as prospective applicants for next year trying to figure out what on earth a college is and which one they should apply to. As a wizened final year DPhil student I decided to compile an A-Z of Oxford related terms in the hope that someone might find it useful.
A – Ashmolean Museum
Britain’s first public museum, established all the way back in 1678. Home to exhibits covering Ancient Egypt to Modern Art and everything in between.
B – Battels
A termly bill students receive from their college which might cover things like charges for food and accommodation, or fines for not returning books to the library on time.
C – College
The 39 colleges are small educational institutions which together comprise the University of Oxford. Every student is a member of a college, each of which has their own set of facilities, including a dining hall, bar, library and student accommodation. Colleges also have their own student unions, called the Junior Common Room (for undergraduates) and Middle Common Room (for postgraduates), which are excellent places to socialise and meet people studying lots of different subjects.
An idea by any other name would smell as sweet.
A blog post about ideas.
Ideation is the formation of an idea, but how do we ideate?
The route of the word is “to see”, so when we have an idea we see something. In that moment of realization, we hold on to something quite abstract. Some describe it as a click or pattern or insight. This “seeing” is with the mind, however, not the eyes. Idea also implies sentiment or direction – a path one might say. It’s this last point that resonates with me most. When we are lost, in the sea of thoughts, most of the time the consequences are immediate (no consciousness required). However, sometimes we must pause and ideate. Our path, the next step, is unclear.
Continue readingWhy all academics should be on TikTok
Recently I have had the opportunity to get a closer look at the submission, review and promotion cycle for a typical academic paper. It was a great learning experience and led to an increase in the number and of research papers, news articles, and reviews I read in preparation. However, on multiple occasions, I did think “I wish I could watch a 2 min video to explain this”. That got me thinking, why couldn’t I and should I be able to?
Being Brief.
This is a blog post about using fewer words.
Continue reading2021 likely to be a bumper year for therapeutic antibodies entering clinical trials; massive increase in new targets
Earlier this month the World Health Organisation (WHO) released Proposed International Nonproprietary Name List 125 (PL125), comprising the therapeutics entering clinical trials during the first half of 2021. We have just added this data to our Therapeutic Structural Antibody Database (Thera-SAbDab), bringing the total number of therapeutic antibodies recognised by the WHO to 711.
This is up from 651 at the end of 2020, a year which saw 89 new therapeutic antibodies introduced to the clinic. This rise of 60 in just the first half of 2021 bodes well for a record-breaking year of therapeutics entering trials.
Continue readingA Smattering of Olympic Trivia!
Tokyo 2020 is now firmly in our rearview mirror, and I for one will be sad to be deprived of the opportunity to wake up at 4AM to passionately cheer on someone I’ve never heard of in an event I know nothing about as they go for Gold. The heyday of amateurism in the Olympics may be long gone, but it’s never been better for the amateur fan, with 24/7, on-demand, coverage, unprecedented access to the athletes via social media and remote working offering the opportunity to watch the games on a second screen without worrying about one’s boss noticing (not that I would ever engage in such an irresponsible practice, in case my Supervisor is reading this…).
To indulge both my post-Olympics melancholy and my addiction to sports trivia, I’ve trawled the internet to find some interest factoids related to the Summer Games and present them below for your mild enjoyment:
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AlphaFold 2 is here: what’s behind the structure prediction miracle
Nature has now released that AlphaFold 2 paper, after eight long months of waiting. The main text reports more or less what we have known for nearly a year, with some added tidbits, although it is accompanied by a painstaking description of the architecture in the supplementary information. Perhaps more importantly, the authors have released the entirety of the code, including all details to run the pipeline, on Github. And there is no small print this time: you can run inference on any protein (I’ve checked!).
Have you not heard the news? Let me refresh your memory. In November 2020, a team of AI scientists from Google DeepMind indisputably won the 14th Critical Assessment of Structural Prediction competition, a biennial blind test where computational biologists try to predict the structure of several proteins whose structure has been determined experimentally but not publicly released. Their results were so astounding, and the problem so central to biology, that it took the entire world by surprise and left an entire discipline, computational biology, wondering what had just happened.
Continue readingOne of my other hats – Covid-19 Response Director for UK research and innovation
The group asked me if I would tell them a little bit about one of my other hats at our regular Tuesday meeting, and this blog is about that.
In October 2019 I was seconded part-time to UKRI as the Deputy Executive Chair of the Engineering and Physical Sciences Research council (EPSRC). What is UKRI (UK research and Innovation)? It’s a non-departmental public body that funds research and innovation. It is made up of the seven disciplinary research councils (acronyms to please Tom – AHRC, BBSRC, EPSRC, ESRC, NERC, STFC and MRC), Research England, and the UK’s innovation agency, Innovate UK.
As Deputy Executive Chair of EPSRC I was helping with UKRI strategy, learning how a spending review round works, visiting universities to talk about how they could work better with UKRI – pretty much everything I was expecting to be doing. But like everyone, my world changed in early 2020.
Continue readingHow fast can a protein fold?
A protein’s folding time is the time required for it to reach its unique folded state starting from its unfolded ensemble. Globular, cytosolic proteins can only attain their intended biological function once they have folded. This means that protein folding times, which typically exceed the timescales of enzymatic reactions that proteins carry out by several orders of magnitude, are critical to determining when proteins become functional. Many scientists have worked tirelessly over the years to measure protein folding times, determine their theoretical bounds, and understand how they fit into biology. Here, I focus on one of the more interesting questions to fall out of this field over the years: how fast can a protein fold? Note that this is a very different question than asking “how fast do proteins fold?”
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