Rachel Seongeun Kim
@eunbelivable.bsky.social
🧬Bioinformatician in Steinegger lab, SNU, Korea 🤍Interested in protein structure and software development 🤺Live double life as a fencer
Pinned
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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
Reposted by Rachel Seongeun Kim
We 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/🧵
October 23, 2025 at 1:08 PM
We 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 Kim
Easy 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...
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...
October 16, 2025 at 7:29 AM
Easy 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...
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...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 8:26 AM
Finally we got an end-to-end structural annotation tool for phages!
Reposted by Rachel Seongeun Kim
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...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Rachel Seongeun Kim
Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1
August 7, 2025 at 3:47 AM
Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1
Reposted by Rachel Seongeun Kim
Folddisco 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...
- 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...
July 22, 2025 at 6:11 PM
Folddisco 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...
- 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 Kim
Today 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
📄 www.biorxiv.org/content/10.1...
Also check out poster:
B-50 lolalign Sensitive structural alignments by Lasse
B-123 BFVD by Rachel
Metagenomic-scale analysis of the predicted protein structure universe
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...
www.biorxiv.org
July 22, 2025 at 9:10 AM
Today 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
📄 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 Kim
Our 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
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
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...
www.biorxiv.org
July 21, 2025 at 11:56 AM
Our 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
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/...
📄 academic.oup.com/nar/article/...
July 21, 2025 at 9:36 AM
This time I didn't forget about the stickers. See you soon!
Reposted by Rachel Seongeun Kim
Are 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!
July 7, 2025 at 8:53 PM
Are you a trainee interested in giving a flash talk at the Computational Structural Virology symposium? Abstracts are due in three days, on July 10!
Reposted by Rachel Seongeun Kim
Folddisco 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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
Folddisco 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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Rachel Seongeun Kim
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!
June 12, 2025 at 8:31 PM
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 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.
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.
June 3, 2025 at 12:47 PM
🦠🧬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.
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 Kim
Unicore 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
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
June 3, 2025 at 6:55 AM
Unicore 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
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 Kim
We'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.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
May 15, 2025 at 2:03 PM
We'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.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
Reposted by Rachel Seongeun Kim
An 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-...
🧬🖥️
blog.opentargets.org/an-atlas-of-...
An atlas of tissue-specific protein-protein associations helps to prioritise targets for drug discovery
Pedro Beltrao’s team at ETH Zürich, created the first atlas of protein interactions in 11 human tissues. Mapping which proteins interact in which tissues will help uncover the specific functions of di...
blog.opentargets.org
May 6, 2025 at 10:50 AM
An 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-...
🧬🖥️
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🧭
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
Truly FANTASTIC work!
#RdRpSummit2025
May 12, 2025 at 12:15 PM
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🧭
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🧭
Reposted by Rachel Seongeun Kim
Guess 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!
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!
May 5, 2025 at 1:35 PM
Guess 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!
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 Kim
Introducing 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
The registrations for on-site & remote participation are still open! More info: RdRp.io
#RdRpSummit2025
May 2, 2025 at 2:54 PM
Introducing 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
The registrations for on-site & remote participation are still open! More info: RdRp.io
#RdRpSummit2025
Reposted by Rachel Seongeun Kim
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...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
April 27, 2025 at 12:13 AM
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...
🌐 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!
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!
April 25, 2025 at 7:48 AM
My poster "BFVD" is on 2nd day of RECOMB😁
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
📄 academic.oup.com/nar/article/...
🌐 bfvd.foldseek.com
#RECOMB2025
April 25, 2025 at 5:02 AM
@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
📄 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...
💻🧪🆕
✨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...
💻🧪🆕
April 24, 2025 at 4:07 PM
📢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...
💻🧪🆕
✨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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
March 31, 2025 at 5:07 AM
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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
Reposted by Rachel Seongeun Kim
Metabuli App preprint is out!
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1
March 13, 2025 at 8:51 AM
Metabuli App preprint is out!
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1