There are usually not reports or mentions during the protein design process that it does not match the original design or the oracle that filters it. What does that mean? Anyone have a word for that? Im sure some of you can appreciate that the model and data differ by -1 positions

Tried a workflow to increase productivity. Theres a lot of in silico cloning to do that is between both GUI and text. Give it whatever base vector, define where you want it. Give it the sequences (or have it find them for you) and then output back the final sequences and a table ready for a CRO

Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡@klausenhauser.bsky.social · last mo.

I feel like this is just some babble a untrained bachelor student will spit out. It also gives way too many options. It does show the power of how it can fetch all the data I do use daily, but its just not doing it in the way. I had to even tell it to compare its own designs with the PDB

Excited to try out Claude Science today!!

finally tried it out with Coot 1.3.1 works great! just have to get used to the commands. but I wish there was a mutate binding.

Oli Clarke@olibclarke.bsky.social · 4mo ago

Added custom menus, including one to quickly add common monomers (detergents, buffers etc):

Thanks Claude Cowork! I just replaced 10 hours of searching on Cryosparc and Relion forums with just an afternoon of AI.

A big win for science and sustainable farming in the EU! New Genomic Techniques (NGTs) have the potential to help farmers grow more resilient crops, reduce inputs such as pesticides and fertilisers, strengthen food security, and support a more sustainable agricultural system.

First being a scientist is bad now you’re just banned because you’re a foreigner.. and I paid for the product!

Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡@klausenhauser.bsky.social · 2mo ago

Trying to help someone setup MCP for ChimeraX, wanted to see if Fable can do it. I cant even read a website on it anymore. Opus works fine.

Posted this in LinkedIn. Shameless advert for some new structures 👉 lnkd.in/gT9Be3tH. But more structural biologists here! Nice to have Claude control my ChimeraX. At least for visualizations and analysis I can see it really speeding up things. IF you know what you’re doing and what to ask for.

Trying to help someone setup MCP for ChimeraX, wanted to see if Fable can do it. I cant even read a website on it anymore. Opus works fine.

Always good to remember that the PDB sequence of a structure is not always the sequence of the protein made nor the sequence of the protein analyzed, its the sequence of the protein a human remembered to type in.

CS tools is very handy! Just added another couple of CS tools scripts to my github - one for making adjustable templates for picking membrane proteins in nanodiscs & micelles: github.com/olibclarke/c... (cont. next post:)

Structura Biotechnology@structurabio.bsky.social · 3mo ago

cryosparc-tools is a standalone Python library that connects to #CryoSPARC and is designed to advance your #cryoEM data processing via scripting. 🚀 Watch this new video for an overview of cryosparc-tools, and explore the resources linked in the description 👉 youtu.be/QY7t67c9bQ8

I think LinkedIn Games is the millienial digital crack cocaine…

Two papers in Nature present AI systems that can assist throughout multiple processes involved in scientific research. The systems are designed to assist researchers in accelerating scientific discovery, not to replace them. go.nature.com/4tFHspz go.nature.com/3RQzXyL #Academicsky 🧪

Might enjoy using this tool and see if it’s the model building or innate to the dataset! CrystalBoltz soniaminseokim.github.io/crystalboltz...

Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡@klausenhauser.bsky.social · 4mo ago

Calling all xray structure folks that have worked with denovo proteins. Do you suffer from high rfactors? Myself, someone else I know and now multiple structures all seem to suffer from this. Assuming we all tried our best in model building, what could be some causes?

Phenix 2.1 ❤️Coot 1.2.x

Flower Dump! Lots of Alliums and Irises

I do enjoy this leaf

Another Friday thought. After I was cited unknowingly by some young scientists hundreds of km away 😅 (does this mean I went viral?) “AI: better make it your tool before it starts giving you the instructions”

Calling all xray structure folks that have worked with denovo proteins. Do you suffer from high rfactors? Myself, someone else I know and now multiple structures all seem to suffer from this. Assuming we all tried our best in model building, what could be some causes?

Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬 Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes. The Rule of Thumb: If AF3 can’t model it, we want it.

Ive always been taught verbatim for decades that Glycines are helix breakers, but why is this protein filled of alpha helices so rich in glycines everywhere!

Bye bye dogma? www.science.org/doi/10.1126/...

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two dist...

science.org

Some people cleave tags religiously. This person didnt and made me solve their perfectly structured Histag. Probably also helped in packing. Might have to do experiments without it to show its not an artifact though. Team cleave or not cleave?

I can finally stop cringing and sighing when I hear that sds-page separates only by size as most textbooks say

Magnus Kjærgaard@proteinmagnus.bsky.social · 4mo ago

Why do intrinsically disordered proteins appear larger than they are in SDS-PAGE? We investigate how sequence properties affect SDS-PAGE mobility using synthetic IDRs. Conclusion: We need to consider both SDS binding and the compaction of protein-SDS complexes. www.biorxiv.org/content/10.6...

How much about thermodynamics of AI binders are known? I think this is the first time I’ve seen an endothermic interaction. (Kinetics is fast on fast off) #EMBLProteinQC

Happy that when public services were put to a referendum (proposal to decrease of the annual household charge of 335 CHF (~$430) to 200 for the public broadcaster) that people understood and made the right choice.

Started this project years ago, but now everything is deposited on @addgene.bsky.social and a short @protocolsio.bsky.social is online. Try it out to make your own (cheap) homemade nuclease/Benzonase! dx.doi.org/10.17504/protocols.io.261ged7xov47/v2 Thank you @jcoker10.bsky.social and Michael Lim!

First vacation that I spent more on museums and temples than on food. What a rich cultural history Egypt has spanning millennia

Its that time of the year again OOO

My favourite place this weekend. And some new infrastructure sightings. New train and a new gondola mid level station (nicer than some airports!)