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 readingCategory Archives: Group Meetings
Non-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.
Continue readingThings I’ve Learned from Hosting Speaker Events
For the past couple of years I’ve been involved in running the Oxford University Scientific Society. We host weekly talks in Oxford during the Undergraduate Term, inviting speakers from all scientific disciplines to come and discuss their field with our members. Here are four important lessons I’ve learned from being involved!
Comparative analysis of the CDR loops of antigen receptors
Allow me to present our recently accepted paper: Comparative analysis of the CDR loops of antigen receptors, to appear in Frontiers in Immunology [1]. In the blog post I will give a quick five-minute summary of the key messages in this work.
Continue readingA collection of prion factoids
It’s been several years since I last presented a talk on prions to OPIG, so I thought a neat way of getting up to date would be to read “The prion 2018 round tables“. What’s the current understanding and are we any closer to determining a structure of PrPSc?
Continue readingWhen OPIGlets leave the office
Hi everyone,
My blogpost this time around is a list of conferences popular with OPIGlets. You are highly likely to see at least one of us attending or presenting at these meetings! I’ve tried to make it as exhaustive as possible (with thanks to Fergus Imrie!), listing conferences in upcoming chronological order.
(Most descriptions are slightly modified snippets taken from the official websites.)
OpenMM – easy to learn, highly flexible molecular dynamics in Python
When I came to OPIG this past March I realized I had a novel opportunity – there was no one to tell me which molecular dynamics (MD) program I had to use! Usually, researchers do not have much choice in the matter due to a number of practical concerns. Conflicts between input and output file formats, forces, velocities, and basically everything else between MD suites make having multiple programs flying around tenuous at best if you want group members to be able to help one another. After weighing my options, I settled on OpenMM – and so far I am very happy with the decision.