Rachel Seongeun Kim
🧬Bioinformatician in Steinegger lab, SNU, Korea 🤍Interested in protein structure and software development 🤺Live double life as a fencer
- Reposted by Rachel Seongeun KimFoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
- Reposted by Rachel Seongeun KimMy time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
- Reposted by Rachel Seongeun KimPhold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
- Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...
- Reposted by Rachel Seongeun KimWe train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
- Reposted by Rachel Seongeun KimEasy and interactive taxonomic profiling with Metabuli App. It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop. No command line, server, or internet required. Now published in Bioinformatics! 🧵1/5 doi.org/10.1093/bioi... github.com/steineggerla...
- Finally we got an end-to-end structural annotation tool for phages!
- Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...
- Reposted by Rachel Seongeun KimStoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...
- Reposted by Rachel Seongeun KimProtein Structure Informed Bacteriophage Genome Annotation with Phold biorxiv.org/content/10.1101/202…
- Reposted by Rachel Seongeun KimFolddisco webserver result view update: - Added description texts for AFDB - Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social - Inter-residue distance clustering by DBSCAN to explore motif diversity. 🌐 search.foldseek.com/folddisco 📄 www.biorxiv.org/content/10.1...
- Reposted by Rachel Seongeun KimToday at 2 PM at 3DSIG #ISMBECCB2025, @nbordin.bsky.social presents our joint work on metagenomic-scale clustering and novel domain discovery in predicted structures! 📄 www.biorxiv.org/content/10.1... Also check out poster: B-50 lolalign Sensitive structural alignments by Lasse B-123 BFVD by Rachel
- Reposted by Rachel Seongeun KimOur new preprint is out! www.biorxiv.org/content/10.1... In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide. @podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
- This time I didn't forget about the stickers. See you soon!
- Today at 5pm, @eunbelivable.bsky.social will present her work on the Big Fantastic Viral Database (BFVD) at #ISMB2025 in BOSC. She also has a poster B-123 (tomorrow, 22nd), so please drop by to have ta chat and grab some stickers! 📄 academic.oup.com/nar/article/...
- Reposted by Rachel Seongeun KimAre you a trainee interested in giving a flash talk at the Computational Structural Virology symposium? Abstracts are due in three days, on July 10!
- Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
- Reposted by Rachel Seongeun KimFolddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco
- Reposted by Rachel Seongeun KimHello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
- Reposted by Rachel Seongeun Kim🦠🧬Exciting news! BFVD predicted viral protein structures are now available in @InterProDB! For the first time, explore InterPro functional annotations directly on 3D structures of viral proteins not covered by AlphaFold DB. This bridges a critical gap in structural virology research.
- Reposted by Rachel Seongeun KimUnicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109
- Reposted by Rachel Seongeun KimWe've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments. 🌐 afesm.foldseek.com Read more about the work in the skeetorial 🦋 bsky.app/profile/mart... or our preprint 📄 www.biorxiv.org/content/10.1...
- AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...
- Reposted by Rachel Seongeun KimAn atlas predicting protein interactions in 11 human tissues created by @pedrobeltrao.bsky.social's team at @imsb-eth.bsky.social will help uncover cell-type specific functions, elucidate disease mechanisms, and choose safer targets for drug discovery 🧬🖥️ blog.opentargets.org/an-atlas-of-...
- I cannot say anything what F stands for. I'm thrilled to present BFVD at RdRp summit, finally found right place. Thank you for organizers for inviting to this awesome meeting and city. I would appreciate any feedback and feel free to discuss in-person or cia message. Explore BFVD🧭
- Our next keynote speaker, Rachel Kim, introduces us to BVFD. Now we know what the "F" stands for :) Truly FANTASTIC work! #RdRpSummit2025
- Reposted by Rachel Seongeun KimGuess who is invited as the keynote speaker for the session on "Data Mining & Metadata Analysis"??? It is Rayan Chikhi!!! He will introduce us to Logan. You can read the preprint here: tinyurl.com/vx4cykr7 Registrations are still open for #RdRpSummit2025!
- Reposted by Rachel Seongeun KimIntroducing our invited speaker for the session on 'Viral Dark Matter' we have Rachel Seongeun Kim from the Seoul National University!!!! The registrations for on-site & remote participation are still open! More info: RdRp.io #RdRpSummit2025
- Reposted by Rachel Seongeun KimAFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...
- My poster "BFVD" is on 2nd day of RECOMB😁
- Visit our posters at #RECOMB2025 for: Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis Metagenomics: Classification & Metabuli App GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery & get Marv stickers!
- Reposted by Rachel Seongeun Kim@eunbelivable.bsky.social presented our viral protein structure database BFVD, including the new V2 update with improved predictions using 12 recycles for higher quality structures. Check out the paper and data here: 📄 academic.oup.com/nar/article/... 🌐 bfvd.foldseek.com #RECOMB2025
- Reposted by Rachel Seongeun Kim📢InterPro release 105.0 is live! ✨Update to Pfam 37.3, PROSITE patterns 2025_01 PROSITE profiles 2025_01 and HAMAP 2025_01 ✨342 new entries ✨Addition of InterPro-N annotations ✨Addition of BFVD structure predictions from @martinsteinegger.bsky.social's lab Have a look: ebi.ac.uk/interpro/htt... 💻🧪🆕
- Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3
- V1 improved 178k predictions with <30 homologs in Base-MSA by adding Logan hits. V2 improves confidence through 12 recycles. For each target, we chose the best pLDDT pred from Base, +Logan and +12-recycles. ~4% improved from (very)low to (very)high confidence. Q70LC3 now aligns closely with PDB. 2/3
- Special thanks to @milot.bsky.social , @martinsteinegger.bsky.social , @eli for their kind help and guidance in making this update possible.
