Or: The best lies have a nugget of truth in them.Lucubration – 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 […]
figure making scripts. With these scripts I manage to produce figures that made people question what I had actually been doing with my time – but I promise this will be worth your time.
I have been using with dimensionality reducition techniques recently and I came across this paper by Moon et al. PHATE is a technique that represents high dimensional (ie biological) data in a way that aims to preserve connections over preserving distance and I knew I wanted to try this as soon as I saw it. Why should you care? PHATE in 3D is faster that t-SNE in 2D. It would almost be rude to not try it out.
Detecting atom clashes in protein structures can be useful in a number of scenarios. For example if you are just about to start some molecular dynamics simulation, or if you want to check that a structure generated by a deep learning model is reasonable. It is quite straightforward to code, but I get the feeling […]
As my turn to write a blog post has fallen a few days after April 1st, I decided I would write an April Fools’ Day-inspired post and ask everyone’s favourite chatbot to tell me some jokes. I asked ChatGPT to tell me a knock-knock joke, prompting it with various topics relevant to OPIG (including AI, […]
One of the most treasured group meeting institutions in OPIG is snackage. Each week, one group member is asked to bring in treats for our sometimes lengthy 16:30 meeting. However, as would be the case for any group of 25 or so people, there are various dietary requirements and preferences that can make this snack-quisition […]
When I started my PhD in late 2018, AI hadn’t really entered the field of de novo protein design yet – at least not in a big way. Rosetta’s approach of continually ranking new side chain rotamers on a fixed backbone was still the gold standard for the ‘structure-to-sequence’ problem. And of course before long […]