Martin Steinegger 🇺🇦さんのイラストまとめ

OmegaFold is open source. Thank you so much for releasing it. It installs very easily. On Colab a protein with 583 res. ran out of memory (16GB GPU), 320 worked (it took 13min). 583 ran in ~23m on 24GB GPU. Complex prediction by glycine linker seem to work for a toy example. https://t.co/4NBFFloEgg

ColabFold makes folding with #AlphaFold & #RoseTTAfold accessible to everyone. Our MSA server processed >1.6 million requests to date. We thank the community for all the help to improve Colabfold.

Now published @naturemethods
📄 https://t.co/lzN4heMaaX

ColabFold now uses a faster MMseqs2 backend server. We switched from BFD/Mgnify to ColabFoldDB, a larger metagenomic database, and reduced rate limits a lot, so batch AlphaFold2 runs should be faster.
💻 https://t.co/q4y3N7bxGS

ColabFold now uses the AlphaFold-multimer models paired with MMseqs2 searches for prediction of protein complexes. Just provide chains separated by : and press "Run all" (provide the same sequence multiple times for homooligmers). Check it out at https://t.co/q4y3N7bxGS

Our structural aligner Foldseek can now automatically download databases in a single command. We provide the PDB (#PDB50) and Alphafold DB. You can download Foldseek here: https://t.co/HVRSi3ycX3

foldseek databases PDB pdb tmp
foldseek easy-search query.pdb pdb aln.m8 tmp

Conterminator a method to terminate contamination in genome and protein databases is published @GenomeBiology.
@StevenSalzberg1 and me found >114K/2M likely contaminations in RefSeq/GenBank.
📃 https://t.co/uX6UhVOEWh
💾 https://t.co/y572X4HIBB
🐍 conda install conterminator

The metagenomic method trilogy is complete and the end of my PhD is near :)
(1) MMseqs2: Fast and sensitive search
https://t.co/hVgttgausy
(2) Linclust: Linear time clustering
https://t.co/krgpCvf1UN
(3) Plass: Protein level assembly
https://t.co/7RgScBAgto