Christopher Ing

Scientists: answering the questions we were dying to know, but too afraid to ask

There's a form of "Personal Computer" Stockholm syndrome where an accumulation of weird tech issues makes computer use border on torture, with a surprising user tolerance threshold. Usually it's only identified by a 3rd party using your machine and remarking... "How the heck do you use this thing?"

"The Illiad" is kinda like "Three-Body Problem" in that their both about vengeful omnipresent beings fucking around with physics on earth.

Sequence logo's are so underutilized, even in protein design papers. Mainly because all the libraries to create them have zero imagination for applications. Represent ensembles of any residue-level property with symbol/color, or use pos/neg enrichment to show differential bias between any two sets!

Grant me the confidence of a scientist asking for help installing software in the Boltz2 webinar Zoom chat

Increasingly convinced there's collusion in "big spinach" to sell washed leaves "wet" in grocery store tubs to accelerate rot and increase sales 🤫🥬💧🤑

M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale

leetspeak still alive in the bioinformatics community, academic.oup.com/nar/advance-...

Kinda like mining bitcoin

Love and respect the four-digit PDB code convention, and will miss it. I like how you can use it to roughly "date" structures. Like, 3J5P as a marker for the start of the cryo-EM membrane protein era in 2013.

As if the big scientific publishers weren't bad enough, they sometimes just take journals offline. "Current Opinion in Drug Discovery & Development" ran from 1998-2010. Owned by Thomson but almost all links are broken with no other hosts (that I can tell), pubmed.ncbi.nlm.nih.gov?term=%22Curr...

Biology is hard example #103342: "Our in vivo screening efforts confirmed the requirement for high-affinity binding of the ligand for the cognate receptor to achieve robust activity" (*whisper* R^2 of 0.14) academic.oup.com/nar/article/...

Pharma: "Drug discovery is so hard, we have great binders but they fail in preclinical and clinical research"
AI Drug Discovery companies: "So... if we make better binders all diseases will be cured?"

Oral-B Pro 1000 and Philips Sonicare 4100 are the canonical "best electric toothbrushes", but they are really different UX. Philips brush size and vibration is so small it's basically regular brushing with a buzz, but with the Oral-B its truly elevated brushing on easy mode (not a paid advert!)

Academic in Bio ML: "Oh rats, my inverse design sequence recovery metric is really poor on this complex... better lower the temperature."

Biotech patent: "In some embodiments, our claim is the endogenous ligand and anything over 20% identity. Trust me look at all these sequences we generated."

In the zone. Completely in sync with the universe. Measured the same weight on my digital scale 3 days in a row. That's even harder than losing or gaining weight 👏👏

How many yogurt lid related cuts go unreported each year due to shame/disgrace? Destigmatize yogurt lid related injury and hold the diary industry accountable.

It's probably been said before, but random Reddit comments with like 1 upvote have a lot of power for specific recommendations. For example, trip planning: city A vs B, or hotel A vs B. Is there any better source of "truth" than these anecdotes? They can rank high on search, pretty empowering...

"I'll be candid: by now you know I care about you personally, but I need to challenge you directly so my behavior doesn't come across as ruinously empathetic or obnoxiously aggressive. Really, it's the only way I can give you feedback so I can sincerely manipulate. Do you have any feedback on that?"

Okay, so it's almost a year after AF3 reported ~75% accuracy on structural prediction of glycosylation. What's the status update on predicting the glycosylated structural proteome?

"Our founding team has combined experience of 20K A100 GPU years"

Excellent study on peptide discovery and characterization, but I was not expecting the computational heavy-lifting of their prediction methodology to be... regex 😜 github.com/Svensson-Lab...

The art of writing a high impact manuscript, github.com/RosettaCommo...

In the VantAI webinar on Boltz-1 the authors describe challenges of arbitrary depositor-defined protein assemblies. Headaches incoming when they discover assembly is also dependent on experimental conditions 😅 E.g. www.biorxiv.org/content/10.1...

Academics may not appreciate the impact of licensing ML models/weights non-commercial use. I've *not* experimentally tested thousands of data points from predictive models because of it. Probably impossible, but there should be a license that requires anonymized validation data to flow to authors.

Cryo-EM structure of the calcium-sensing receptor complexed with the kokumi substance γ-glutamyl-valyl-glycine - Scientific Reports Scientific Reports - Cryo-EM structure of the calcium-sensing receptor complexed with the kokumi substance γ-glutamyl-valyl-glycine

Ajinomoto Co doing flavour R&D on a whole other level...

How do you scramble a peptide binder? Not by randomly scrambling the sequence! Must account for binding motifs (can have gaps), physicochemical similarity, structure, sequence complexity, chemical identity (like NCAA anchor residues). Chirality-swapped retro-inversions are not a silver bullet...

The field needs a benchmark for benchmarking datasets that ensures collections of data have high scores for data relevance, diversity, quality, and standardization, balanced splits, data annotation, reproducibility, and evaluation metrics; otherwise we're in for "yet another"...

ChatGPT: "Conformational monism" denotes a belief system or viewpoint that a given protein sequence has only one definitive, biologically relevant 3D conformation. Ex. The researcher remained a conformational monist, insisting that their AlphaFold2 model was sufficient to explain structure-function.

New Trends in Brain Shuttle Peptides The pharmacological treatment of central nervous system diseases faces significant challenges due to the presence of the blood–brain barrier (BBB). This barrier naturally protects the brain and preven...

Brain shuttle peptide literature is like "the mechanism is through specific receptor targeting and receptor-mediated endocytosis" yet... both T7 and Angiopep-2 function in both L- and D- forms. What's up with that? pubs.acs.org/doi/10.1021/...

First-gen LLMs: hallucinated text, made-up citations
Retrieval-augmented generation equipped LLMs: generic summary text with linked documents
Next-gen LLMs: reasoning tokens (hidden) with ranked documents (a.k.a. gone full-circle back to web search)