Lightnews — Scholar-powered news

Rachel Seongeun Kim @eunbelivable.bsky.social · Aug 8

Finally we got an end-to-end structural annotation tool for phages!

George Bouras @gbouras13.bsky.social · Aug 8

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...

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

1 11

Reposted by Rachel Seongeun Kim

George Bouras @gbouras13.bsky.social · Aug 8

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...

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

5 65 130

Reposted by Rachel Seongeun Kim

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Aug 7

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

10 13

Reposted by Rachel Seongeun Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 22

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...

14 36

Reposted by Rachel Seongeun Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 22

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

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

2 8 36

Reposted by Rachel Seongeun Kim

Chan Yeong Kim @chanyeong-kim.bsky.social · Jul 21

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

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

1 18 28

Rachel Seongeun Kim @eunbelivable.bsky.social · Jul 21

This time I didn't forget about the stickers. See you soon!

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 21

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/...

7

Reposted by Rachel Seongeun Kim

Jason Nomburg @jnoms.bsky.social · Jul 7

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!

Jason Nomburg @jnoms.bsky.social · Jun 12

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!

1 3 2

Reposted by Rachel Seongeun Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 7

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

8 70 150

Reposted by Rachel Seongeun Kim

Jason Nomburg @jnoms.bsky.social · Jun 12

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!

2 52 68

Reposted by Rachel Seongeun Kim

InterPro @interprodb.bsky.social · Jun 3

🦠🧬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.

CATH-Gene3D annotation visualised on BFVD structure prediction of UniProt A0A075FDU7

2 9 29

Reposted by Rachel Seongeun Kim

Dongwook Kim @dongwookkim.bsky.social · Jun 3

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

3 31 68

Reposted by Rachel Seongeun Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · May 15

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...

2 22 60

Reposted by Rachel Seongeun Kim

Open Targets @opentargets.org · May 6

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-...

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

10 18

Rachel Seongeun Kim @eunbelivable.bsky.social · May 12

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🧭

RdRp Summit @rdrpsummit.bsky.social · May 12

Our next keynote speaker, Rachel Kim, introduces us to BVFD. Now we know what the "F" stands for :)
Truly FANTASTIC work!
#RdRpSummit2025

2 10

Reposted by Rachel Seongeun Kim

RdRp Summit @rdrpsummit.bsky.social · May 5

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!

4 9

Reposted by Rachel Seongeun Kim

RdRp Summit @rdrpsummit.bsky.social · May 2

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

1 12 25

Reposted by Rachel Seongeun Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Apr 27

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...

4 71 140

Rachel Seongeun Kim @eunbelivable.bsky.social · Apr 25

thank you so much😁

1 1

Rachel Seongeun Kim @eunbelivable.bsky.social · Apr 25

My poster "BFVD" is on 2nd day of RECOMB😁

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Apr 25

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!

1 1

Reposted by Rachel Seongeun Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Apr 25

@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

1 8 22

Reposted by Rachel Seongeun Kim

InterPro @interprodb.bsky.social · Apr 24

📢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...
💻🧪🆕

Databases updates
Pfam 37.3
PROSITE patterns 2025_01
PROSITE profiles 2025_01
HAMAP 2025_01

New entries
342 new entries with:
318 Pfam
40 NCBIfam
12 Prosite profiles
6 PANTHER
5 CDD

New features
InterPro-N annotations
BFVD structure predictions
Simplified structure pages

1 10 19

Rachel Seongeun Kim @eunbelivable.bsky.social · Mar 31

Special thanks to @milot.bsky.social , @martinsteinegger.bsky.social , @eli for their kind help and guidance in making this update possible.

5

Rachel Seongeun Kim @eunbelivable.bsky.social · Mar 31

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

1 3

Rachel Seongeun Kim @eunbelivable.bsky.social · Mar 31

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

2 24 65