Recently, I’ve been using a Convolutional Neural Network (CNN), and other methods, to predict the binding affinity of antibodies from their sequence. However, nine months ago, I applied a CNN to a far more important task – distinguishing images of butter from margarine. Please check out the GitHub link below to learn moo-re.
https://github.com/lewis-chinery/AI_cant_believe_its_not_butter
We’ve been investigating deep learning-based protein-ligand docking methods which often claim to be able to generate ligand binding modes within 2Å RMSD of the experimental one. We found, however, this simple criterion can conceal a multitude of chemical and structural sins…
DeepDock attempted to generate the ligand binding mode from PDB ID 1t9b
(light blue carbons, left), but gave pretzeled rings instead (white carbons, right).
I don’t believe punting comes up much in Biggie Smalls’ raps (we live a pretty shielded life here in Oxford). Nevertheless, here are some photos from our recent OPunting trip, paired, very questionably and entirely for the pun’s sake, with some of the titles of songs he wrote/featured in.
Continue readingWhen showcasing an approach in computational chemistry, an example molecule is required as a placeholder. But which to chose from? I would classify there different approaches: choosing a recognisable molecules, a top selling drugs, or a randomly sketched compound.
At a recent conference, Sheffield Cheminformatics 2023, I saw examples of all three and one problem I had that some placeholders distracted me into searching to figure out what it was.
Continue readingEver wondered whether opiglet keep their ketchup in the fridge or cupboard. Perhaps you’ve wanted to know how to create nice figure to display lots of information simultaniously. Publication quality figures are easy within R with the ggplot package. We may also learn some good visualisation.
Continue readingIf you are running lots of little jobs in SLURM and want to make use of free nodes that suddenly become available, it is helpful to have a way of rapidly shipping your environments that does not rely on installing conda or rebuilding the environment from scratch every time. This is useful with complex rebuilds where exported .yml files do not always work as expected, even when specifying exact versions and source locations.
In these situations a tool such a conda-pack becomes incredibly useful. Once you have perfected the house of cards that is your conda environment, you can use conda-pack to save that exact state as a tar.gz file.
conda-pack -n my_precious_env -o my_precious_env.tar.gz
This can provide you with a backup to be used when you accidentally delete conda from your system, or if you irreparable corrupt the environment and cannot roll back to the point in time when everything worked. These tar.gz files can also be copied to distant locations by the use of rsync or scp, unpacked, sourced and used without installing conda…
Continue readingLucubration – The action or occupation of intensive study originally by candle or lamplight.
Gaslighting – Psychological abuse in which a person or group causes someone to question their own sanity, memories, or perception.
I was recently having a play with Google Bard. Bard, unlike ChatGPT has access to live data. It also undergoes live feedback and quality control. I was hoping to see if it would find me any journals with articles on prion research which I’d previously overlooked.
Me: Please show me some recent articles about prion research.
(Because always be polite to our AI overlords, they’ll remember!)
I don’t know if anyone out there shares this peculiar hobby of mine (God, I hope not!), but I often find myself scouring the depths of the internet for some truly bizarre academic papers. Though there is an endless supply of such content to keep one entertained (read: distract yourself during those afternoons you planned to be productive but ended up succumbing to the lunch food coma), I’ve managed to compile a short list of the most fascinating ones for your enjoyment!
This fantastic and robust study examines the enigmatic phenomenon of disappearing teaspoons in a shared kitchen—an issue of acute importance to all of us who rely on these tiny utensils. The authors reveal the shocking truth about teaspoons’ shockingly short half-life in research institutes. The question remains: does this phenomenon extend to other cutlery as well?
Continue readingOPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).
Continue readingAlternative titles:
If you are like me, you can happily write code for hours and hours on end but as soon as you need to write a paper you end up staring at a blank page. Luckily, I have come up with a fool proof way to trick myself into thinking I am coding when in reality I am finalling getting around to writing up the work my supervisor has been wanting for the last month. Introducing Latex and git- this was my approach to draft a review paper recently and in this blopig post I will go through some of the ups and downs I had using these tools.
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