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 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:…

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.

☝️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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