A couple of weeks ago I was lucky enough to be asked to speak at the 5th Computational Drug Discovery & Development for Biologics Summit. This was my first virtual conference – it was a shame I didn’t get to visit Boston, and presenting to my empty room was slightly bizarre, but it was great to hear what people have been working on, and there’s definitely something to be said for attending a conference in fluffy socks…
I recently completed an internship during which I spent a considerable amount of time doing software engineering. One of my main take-aways from this experience was that in industry, a lot more attention is spent on ensuring that code committed to a GitHub repo is clean and bug-free.
This is achieved through several means like code review (get other people to read your code), test-driven development (make sure your code works as you are adding functionality) or paired development (have two people work together on the same piece of code). Here, I will instead focus on a useful tool that is easy to integrate into your existing git workflow: Pre-commit hooks.
Continue readingThe start of Michaelmas Term means some new faces on our Zoom screens and lots of things for our new group members to get used to. To help them settle in quickly I thought I’d put together an updated edition of the 10 Commandments of OPIG, tailored towards our new reality.
Continue readingIn preparation for remote teaching this year, I’ve spent the last few weeks converting the Doctoral Training Centre’s ‘Introduction to Computer Programming’ course into a series of Jupyter notebooks so that the course can be run entirely using Google Colaboratory.
Continue readingFragment-based drug discovery (FBDD) is based on the idea that using small (< 300 Da), highly soluble compounds to screen against a target will give higher hit rates and sample chemical space more efficiently compared to screens using larger, drug-like compounds.
Excel’s pervasiveness has resulted in it being used (correctly or incorrectly) in just about every area of science.
Unfortunately, Excel has some traps for the new player and unless you’ve fallen for them before, they are not entirely obvious. They stem from the fact that Excel will try to help the user by reformatting data into what it thinks you mean.
Continue readingSelectivity is an important trait to consider when designing small molecule probes for chemical biology. If you wish to use a small molecule to study a particular protein, but that small molecule is fairly promiscuous in its binding habits, there are risks that any effects you observe may be due to it binding other proteins with similarly shaped binding pockets, instead of your protein of interest.
Continue readingIn my work, I mainly look at antigen-bound antibodies and this means a lot of analysing interfaces. Specifically, I spend a lot of my time examining the contributions of complementarity-determining regions (CDRs) to antigen binding, but what about antibodies where the framework (FW) region also contributes to binding? Such structures do exist, and these interactions are rarely trivial. As such, a recent preprint I came across where the authors examined the DE loops of antibodies was a great motivator to broaden my horizons!
Continue readingIn the past few months we have seen a lot of papers reporting antibodies that they found to bind to SARS-CoV-2 (a database can be found here: http://opig.stats.ox.ac.uk/webapps/covabdab/). Some of them were from the analysis of a patient’s immune system. Some of them come with crystal structures to show where they bind. Some don’t have structures, but they have the sequences and some competition assay data to show approximately where on the spike protein they bind. The main focus is around an area called the Receptor Binding Domain (RBD) which is where the spike protein engages the human ACE2 receptor and causes the downstream problems. In this paper, the authors ran a complete mutagenesis on the RBD of the SARS-CoV-2 spike protein.
Continue readingSince my last blogpost on this topic back in 2018, OPIG has expanded its range of tools for antibody/BCR analysis. Here is an updated summary of the OPIG antibody databases and immunoinformatics tools.
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