Developing data intensive computational methods • PI @ Seoul National University 🇰🇷 • #FirstGen • he/him • Hauptschülerhttps://bsky.app/profile/martinsteinegger.bsky.socialhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mukhxqv2pk2gAlphaFold2-WebGPU now supports AlphaFold-Multimer. As in ColabFold, simply use : to separate chains in the sequence input. It is also becoming much more stable: I was able to predict a 491-aa protein in ~4 minutes in M4 Pro. Chrome currently performs better than Firefox for WebGPU, unfortunately. [contains quote post or other embedded content]02 Sep 2026 17:36 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mukhxqv2pk2ghttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mucqcxx7ms2qRun AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 https://martin-steinegger.github.io/alphafold2-webgpu/30 Aug 2026 15:45 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mucqcxx7ms2qhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mtyu4pv7qk2yFoldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 https://www.biorxiv.org/content/10.64898/2026.08.24.746585v1 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com26 Aug 2026 17:26 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mtyu4pv7qk2yhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mtycgxbqm22pIs @biorxivpreprint.bsky.social broken? We uploaded a preprint, but for some reason the DOI https://doi.org/10.64898/2026.08.24.746585 doesn’t work. Has anyone else run into a similar issue?26 Aug 2026 12:10 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mtycgxbqm22phttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mshuvz63xs2yThe ratio between abstracts accessed and PDFs downloaded @biorxivpreprint.bsky.social was around 2:1, since the abstract page led to the PDF. Now it’s close to 1:2. Does this mean we shift to an LLM based paper exploration? For Riboseek the ratio is even 1:10 (https://www.biorxiv.org/content/10.64898/2026.07.31.741718v1)07 Aug 2026 06:00 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mshuvz63xs2yhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3ms5w3yucqs2yRiboseek has now a WIP Marv Logo! [contains quote post or other embedded content]03 Aug 2026 06:54 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3ms5w3yucqs2yhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3ms22ibo6bk2gRiboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 https://www.biorxiv.org/content/10.64898/2026.07.31.741718v1 💾 https://github.com/steineggerlab/riboseek 🌐 search.foldseek.com/riboseek01 Aug 2026 18:02 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3ms22ibo6bk2ghttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqrvv6g5fc2i@wheelerlab.org is talking about his effort to build a resource for protein dynamics (PDB for MD). MDRepo is a repository to store simulation data. This is really needed to push the needle in design, function and more. Please help make it successful by sharing your MD data. #ismb2026 🌐 mdrepo.org16 Jul 2026 18:53 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqrvv6g5fc2ihttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqrpcvwzdk2lMy student @yewonhan.bsky.social will talk today at 3DSIG about our work on expanding the AlphaFold database to complexes (31M predictions). It starts at 14.20 in the International Ballroom East. Please join. We also brought Marv stickers with us. #ISMB202616 Jul 2026 16:56 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqrpcvwzdk2lhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqrl46uckk2d@rolanddunbrack.bsky.social is talking about kinases and interface scoring (ipSAE). AF’s ipTM score avg. PAE over the full area not just the interface, so disorder and extra domains drag it down. ipSAE uses a PAE cutoff to avoid low scores, therefor only consider good interface contacts. #ismb202616 Jul 2026 15:40 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqrl46uckk2dhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqkp7gsmac2aChristopher E. Mason’s keynote at the HitSeq at #ISMB2026 felt like watching an episode of „Sendung ohne Namen“ (does anybody know it?). A crazy amount of ideas, facts, and sci-fi. From environmental metagenomics to space genomics.13 Jul 2026 22:05 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqkp7gsmac2ahttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqkm3lywp22n@yewonhan.bsky.social build a website to explore the #ISMB2026 program. Check it out here: https://yewon-han-bioinfo.github.io/ISMB2026-talks-explorer/13 Jul 2026 21:09 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqkm3lywp22nhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqicdzpq7s2sRichard Durbin starts the #ISMB2026 with his keynote about BWT for genomic search. A walk-through from BWA to his most recent work on pan-genomes GBWT. https://www.biorxiv.org/content/10.64898/2026.03.26.714584v2. Congratulations on the accomplishments by a Senior Scientist Award.12 Jul 2026 23:10 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqicdzpq7s2shttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mqi322jof22xI’m at #ISMB2026 in Washington, DC. Please let me know if you’d like to catch up over coffee.12 Jul 2026 20:59 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mqi322jof22xhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3moub64ohz22rIt seems @anthropic.com or OpenAI are unusable for biological work now. I was considering buying a Teams account, but I am worried it will be useless in the end. Has anybody experience with other LLMs?22 Jun 2026 06:30 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3moub64ohz22rhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3momspbf6u22vICML is happening in Seoul this year, and I’ve been getting several messages about lab visits. Who else will be in town and would like to meet? @milot.bsky.social lab and mine are planning a dinner on July 7th, after the reception. Let me know if you’re interested!19 Jun 2026 07:23 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3momspbf6u22vhttps://bsky.app/profile/martinsteinegger.bsky.social/post/3mnvjj26gkc2sKorea reduces the immigration barriers for foreign researcher https://www.koreatimes.co.kr/southkorea/20260601/korea-expands-top-tier-visa-to-woo-global-scientists Happy to see this happening.10 Jun 2026 01:07 +0000at://did:plc:viwt5ubwv2pmaw2dmlqca5bt/app.bsky.feed.post/3mnvjj26gkc2s