Discover and read the best of Twitter Threads about #Alphafold2

Most recents (6)

Some initial results from the #CASP15 competition and we see that #Alphafold2 has become a fertile ground for experimentation by several research groups around the world. Facebook's ESM protein language models (pLMs) are the top non-MSA based methods.
Another slide showing some of the experimentation taking place: increase the number of models, recycles, get more diversity using dropout (how would that work?), subsample MSAs.
A slide showing the amount of #GPU hours used for computing the structures in the #CASP15 dataset.
Read 6 tweets
We are extremely pleased to present something quite new from our team. In these TWO @biorxivpreprint, Mark Roosjen, @AndreKuhn8 @WUR and colleagues report the existence of an ancient, rapid auxin response system, its regulators and function. A Tweetorial… (1/23)
Wonderful work by many colleagues has pieced together a response system for the plant signaling molecule auxin to regulate gene expression, a mechanism that found applications in animal cell biology (auxin degron). Two reasons convinced us that another system must exist…(2/23)
First, many cellular responses are simply too fast to involve gene expression. Second, algae respond to auxin, but lack known response proteins elifesciences.org/articles/33399. We hypothesized that an intrinsically rapid system is conserved between land plants and algae… (3/23)
Read 23 tweets
Pretty wild that there have been at least 4-5 antibody-specific structure prediction tools this year, all based on #deeplearning

1. DeepAb/IgFold (@jeffruffolo)
2. ABLooper/ImmuneBuilder (@brennanaba)
3. Equifold (@jaehyeon_lee_ml)
4. t-AbFold

What does this mean? 🧵(1/6)
First, it's pretty crazy we even have antibody-specific tools, since #AlphaFold2, #ESMFold, #OmegaFold, all do a decent job at antibody modelling. However, antibody-specific tools have -some- feature that's necessary (e.g. being MSA-free) (2/6)
The demand is likely due to interest from pharma & biotech, but we don't have anywhere near the same level of interest for other polymorphic proteins like TCRs and MHCs (🤔). Regardless, with such interest, I think an antibody-specific CASP should be resurrected! (3/6)
Read 7 tweets
NEW: This Post Was Written By #AI: sjtylr.net/2022/10/08/thi…

From idea to content and published post in under 30mins, using free tools. This tech is developing *fast* and will have implications for teaching, learning and our graduates.

#EdTech
☝️Using tools from @playground_ai @peppertype_ai @AiWritesonic @copy_ai and inspired by @Suhail @kaifulee @FryRsquared @DeepMind @daniel_eckler and more. Follow them all for super-interesting news. #AI
Read 305 tweets
Two large #antitrust probes in the same screenshot that relate to #Genomics and #Bioinformatics
(1) Possible buyout of #ARM by #NVIDIA does have an effect on the #Bioinformatics field: many applications now are deployable on CPU/GPUs with #ARM and/or #NVIDIA chips on them. Some recent examples are:
(a) the Oxford @nanopore MinION Mk1c device, which originally was specced at Jetson TX2 ARM+Pascal GPU accelerators (ARM processor 6 cores, 256 Core GPU), 8 GB RAM (may have changed since then.
Read 42 tweets
Since the publication of #AlphaFold2 and #RoseTTAFold and now that the tools and models have been made accessible, there has been an avalanche of attempts to solve old crystal structures. This thread covers tips from the #PhaserTeam for doing #MR with these models. (1/...)
The first thing to be aware of is that the B-factor fields contain measures of confidence in the correctness of the prediction, not actual B-factors. This means: 1) we can use that confidence to trim the model and 2) we need to convert that to an appropriate B-factor. (2/...)
Phaser will take those B-factors and use them to weight the different parts of the model. This can improve your chances of success with the model. (3/...)
Read 11 tweets

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