We have two cats at home, one of which habitually roams around the neighbourhood. This prompted my mother to have concerns about animals and specifically pets as carriers of the virus so I thought I’d read up a bit on this.
Continue readingElectrostatic interactions govern extreme nascent protein ejection times from ribosomes and can delay ribosome recycling
Finishing up a lingering project from your PhD almost a year into your postdoc is a great feeling, especially when it has actually been about 3 years in the making.
Though somewhat outside of the usual scope of activities in OPIG, I encourage you to take a look if the below summary grabs your interest. The full paper and supporting materials (including some movies which took entirely too long to make) can be found at https://pubs.acs.org/doi/abs/10.1021/jacs.9b12264.
When antibodies go wrong: how antibodies can help viruses infect cells
I’ve been keeping up to date with the latest coronavirus vaccine developments using Derek Lowe’s blog, a resource which I cannot recommend highly enough. A recent post mentioned that vaccines developers are looking out for signs of antibody-dependent enhancement (ADE), which I vaguely remembered from my undergraduate biochemistry days researching an essay on dengue fever. ADE is an interesting immunology phenomenon, and so I thought I’d treat you all to a brief introduction to the issue.
Continue readingThe Coronavirus Antibody Database (CoV-AbDab)
We are happy to announce the release of CoV-AbDab, our database tracking all coronavirus binding antibodies and nanobodies with molecular-level metadata. The database can be searched and downloaded here: http://opig.stats.ox.ac.uk/webapps/coronavirus
Continue readingMore tales of 3D printing
Science in the Time of COVID-19
If you are reading this blog, I am sure you will agree that science and research are essential, and even more in the context of a pandemic. Concepts such as PCR, antibody, and herd immunity are slowly getting into people’s vocabulary. This fact makes me quite happy but puts in evidence the lack of scientific knowledge among the population.
Continue readingHERO proteins are here to save you (assuming you’re another protein or a fruit fly)
For one of OPIG’s short talks, I recently introduced the work done by Kotaro Tsuboyama et al. found in the paper A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. As the name implies, HERO proteins have been found to retain function even after being boiled at 95C and have been found both in Drosophila and human HEK293T cell lines. Whilst it’s not impossible to find proteins which can “survive” 90+ Celsius, these are expected to be the reserve of extremophiles, not found in humans or fruit flies.
Continue readingDon’t drink bleach, don’t share canards!
Beyond the thousands of deaths and the millions of infected people, the COVID-19 pandemic has quickly transformed Western society. This virus has provoked the confinement of millions of people in their houses, the closure of bars, restaurants, and pubs, schools, museums, and theatres. However, for this post, I will focus on another side effect of the pandemic: the spread of canards, which flow even faster than the virus itself.
Continue readingNon-specialist intro: Convalescent sera and some thoughts on its relevance to structural biology
A couple of weeks ago, I gave a group meeting talk on my current research. Interestingly most of the questions I received were not directly related to my research methods, but rather, on the broader application of antibody-related therapies, as I used the example of convalescent sera as a potential ‘quick fix’ in the current COVID-19 pandemic, to motivate why antibody research is important! So I thought in this blog post, I would give a quick introduction to convalescent sera. (Disclaimer: This does not contain any clinical information.)
Continue readingUnderstanding the synthesizability of molecules proposed by generative models
De novo molecular design is a computational technique to generate molecules with desired properties from scratch. Classical generative algorithms are based on Genetic Algorithms (GA) and the iterative construction of molecules from molecular fragments. Recently, Variational Auto-Encoders (VAEs), Generative Adversarial Networks (GANs) have been developed for this task, however, the synthesizability of the proposed molecular structures remains an issue. Gao and Coley[1] provided an analysis of the synthesizability of the molecules proposed by these de novo generative algorithms, and discuss their strengths and weaknesses.
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