I came across a recent paper on the antibody-protein binding and conformational changes. As I work mainly on the binding site/Fv regions of antibodies, I am intrigued to see the role of the constant domains in the overall antibody function.
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Prerecording Conference Talks and Posters using OBS Studio
Seemingly every conference due to take place this year has either been cancelled or will be run virtually due to the COVID-19 pandemic. Many organisers have decided that running entirely live virtual programmes causes more trouble than it’s worth (e.g. due to unforseeable IT and internet issues disrupting the schedule), and so are asking their presenters to prerecord their talks, which are then broadcast “live” on the day.
I recently “presented” two virtual prerecorded talks at the ISMB conference using Open Broadcast Software Studio (OBS Studio), a free open-source software package most commonly used by live-streamers on Twitch and Youtube. It is super simple to use and achieves a professional output, with video overlaying a presentation slide deck/poster PDF. This blog is a “how-to” on getting started with OBS for conference talks/poster presentations.
Continue readingObserved Antibody Space + miAIRR
Today is the day for another (potentially penultimate) blog post from me. Using this opportunity, I would like to introduce to you our recent update to the Observed Antibody Space (OAS) resource.
Continue readingWhere do OPIGlets come from?
Now you might think the answer to this question is OSOWs, but in fact they come from a wide variety of Undergraduate degrees!
The 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 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 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 readingMolecular dynamics analysis in MDAnalysis
Any opportunity to use rigorously tested and supported analysis tools rather than in-house code is, in my opinion, an opportunity you owe it to yourself to explore.
My preferred tool for analyzing the output of molecular dynamics (MD) simulations is MDAnalysis, a Python library that provides robust and easy-to-use tools for analyzing most common files output by MD packages (including PDB, DCD, COR, and XTC file formats). But, of course, MDAnalysis can analyze any PDB file, not just one output from an MD simulations. There may be an opportunity in your workflow to incorporate MDAnalysis to save time or to provide more robust error handling than whatever in-house code you currently use.
This Group is Tired of Comic Book Movies : An OPIGlet’s appeal to the DC and Marvel Corporations.
A previous OPIGlet discussed biscuits in his blog post.
Not to be outdone, I will now discuss something even more nerdy: new avenues for comic book adapations. For brevity’s sake, this OPIGlet will focus on the DC and Marvel Corporations as key examples.1
Journal Club: Is our data biased, and should it be?
Last week I presented the above paper at group meeting. While a little different from a typical OPIG journal club paper, the data we have access to almost certainly suffers from the same range of (possible) biases explored in this paper.
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