Christoph Elfmann

Finally fixed some issues with PTMs for the PAE Viewer! Instead of the per-atom PAE which #AlphaFold outputs for modified amino acids, the average per-residue PAE is now displayed. subtiwiki.uni-goettingen.de/v4/paeViewerDe…

@CommichauM @IMPRS_GS @uniGoettingen Genau! Dachte, die Dreiecksform macht sich ganz gut für den Beispiel-Screenshot

@c_elfmann @IMPRS_GS @uniGoettingen Sehr cooles feature von #subtiwiki ! Das ist doch die Struktur von DarA, oder?

Try out our integration of the amazing protein structure search tool #Foldseek on #SubtiWiki (subtiwiki.uni-goettingen.de/v5/foldseek)! Just upload a structure or use PDB/AlphaFoldDB entries to find similar structures. @IMPRS_GS @uniGoettingen #alphafold #bacillus #subtilis

Now you can also find me on @bluesky (bsky.app/profile/c-elfm…) and @joinmastodon (@elfmann" target="_blank" rel="nofollow noopener">academiccloud.social/@elfmann)!

@schnamori @SoedingL @thesteinegger @milot_mirdita And of course many thanks to @clmgilchrist and Woosub Kim for their work on the search server and on Foldseek-Multimer, respectively, which was used in our implementation!

Thanks a lot to Michel van Kempen, Stephanie Kim, @schnamori, @SoedingL, and @thesteinegger for the development of Foldseek! Also check out the fantastic search.foldseek.com by @milot_mirdita, which we used as a blueprint. It boosts more options and detailed evaluation!

The PAE Viewer (subtiwiki.uni-goettingen.de/v4/paeViewerDe…) now supports evaluation of ligands and PTMs in your AlphaFold predictions, and the display of DNAs/RNAs is improved! @IMPRS_GS @uniGoettingen #alphafold #subtiwiki

I've created an offline version of the PAE Viewer with a basic CLI via Python, which you can use in your scripts. It just takes the input and opens the page in the browser with the data preloaded. Check out the new "Offline version" tab for instructions! subtiwiki.uni-goettingen.de/v4/paeViewerDe…

Don't worry if you're missing some features in this newest version, the last version is still accessible. Editing of data is also currently only possible in the last version. Many thanks to @VincenzDuMont, Tim van den Berg, Tom Nowak, Janne Pauline Winsemann and many more!

Proudly announcing the early release of SubtiWiki v5 (subtiwiki.uni-goettingen.de)! It has many new features which we hope you'll like. It also still might have some bugs / missing data, so please don't hesitate to let us know! #subtiwiki #bacillus #subtilis @IMPRS_GS @JorgStulke

@jankosinski @RuneKidmose Hi! Unfortunately, it's just a simple script which opens the PAE Viewer as a web page right now. So it can't be easily embedded (except maybe with iframe's?). For now it just makes it easier to use in pipelines. Hopefully I can make a more versatile version in the future 👍

@RuneKidmose @c_elfmann Ah ok! We will look closer at the pae viewer then! Thanks!

Hi @jankosinski, so @c_elfmann recently made an offline version of his pae_viewer available. So I tried to implement it into my small gui for alphapulldown data. It works really well. tinyurl.com/bd9h74b7

Thank you @DmytroBoik86434 !

Check out the new BLAST search for SubtiWiki's new beta release: subtiwiki.uni-goettingen.de/v5/blast! You can now BLAST your nucleotide/protein sequence against SubtiWiki's coding sequences. Thank you Dmytro Boiko from @UAM_Poznan for your work on it! #subtiwiki #bacillus

Congratulations, ⁦@DennisWicke⁩ , on receiving the thesis award of the Göttingen Center for Molecular Biosciences! ⁦@uniGoettingen⁩ #bacillus #subtiwiki #proudPI

Check the description of the new SubtiWiki framework by @c_elfmann @VincenzDuMont and Tim van den Berg. Enjoy the many new features! @uniGoettingen @IMPRS_GS #SubtiWiki biorxiv.org/content/10.110…

👉 Registration is now open! Please RT and distribute this information among your colleagues! rim2024.uni-hohenheim.de #VAAM #RIM2024 @UniHohenheim

Good evening from Würzburg! I am very much enjoying the @VAAM_Microbes conference with many friends and colleagues. Even presented the poster of @c_elfmann to @CommichauM this afternoon! #subtiwiki

@JorgStulke Just had a look at it, should be solved for now. The server was running out of space 😬I made some adjustments to log & backup configs, it should now take longer until it fills back up again!

There will be 2 opportunities to attend an in-person SubtiWiki workshop at #Grampositive2024 #subtiwiki

However, the feed is only synced once a day, so it can take a while for the newest Tweets to show up.

You can now find a hashtag feed on the sidebar of any gene page! Just use the #subtiwiki hashtag and your Tweet will pop up there!