Kihara Laboratory
@kiharalab.bsky.social
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Bioinformatics, protein modeling, cryoEM, drug screening, function prediction. Daisuke Kihara, professor of Biol/CS, Purdue U. https://kiharalab.org/ YouTube: http://alturl.com/gxvah
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kiharalab.bsky.social
New paper released! "Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints" Yuanyuan Zhang, Zicong Zhang, Y Kagaya, G Terashi, B Zhao, Y Xiong & D Kihara, Communications Biology.
www.nature.com/articles/s42...
kiharalab.bsky.social
New paper from our lab! Introducing EQAFold: "AlphaFold model quality self‐assessment improvement via deep graph learning" Jacob Verburgt, Zicong Zhang & D. Kihara, Protein Science. onlinelibrary.wiley.com/doi/10.1002/...
kiharalab.bsky.social
PNCC Cryo-EM modeling and validation workshop on Sep 3-5, 2025. Register now! tinyurl.com/Cryo-EMModel...
kiharalab.bsky.social
Joon Hong Park received the RCSB poster Prize Award for his presentation at Meeting of the American Crystallographic Association. "EMSuite server: Advanced tools for cryo-EM str modeling, validation and refinement". Congratulations!!
The server: em.kiharalab.org
kiharalab.bsky.social
Summer update of DAQ-Score DB, cryo-EM model quality assessment! Now includes assessment for 251,375 PDB chains from 16,852 EM maps. CCC+Overlap value is now displayed at each entry. daqdb.kiharalab.org
kiharalab.bsky.social
Joon Hong Park presenting his poster at American Crystallographic Association (ACA) 2025 meeting. It is about our cryo-EM structure modeling server.
Visit the server for easy and accurate modeling at em.kiharalab.org
kiharalab.bsky.social
Distpepfold, our new peptide docking method is available as a source code and Google Colab notebook!
Paper: pubs.acs.org/doi/10.1021/...
Github: github.com/kiharalab/Di...
Google Colab: colab.research.google.com/drive/1Q1ecU...
kiharalab.bsky.social
New paper online: Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking | ACS Omega pubs.acs.org/doi/10.1021/...
pubs.acs.org
kiharalab.bsky.social
May update of DAQ-Score DB! Now includes validation reports for 242,447 protein structures from 16190 EMDB maps.
Each entry shows modeling errors in red on the structure plus chain-wise plots.
Check it out: daqdb.kiharalab.org
You can compute DAQ at: em.kiharalab.org
kiharalab.bsky.social
Flash talk by Yuki Kagaya on the Nufold RNA structure prediction method presented at the CASP16 evaluation meeting:
www.youtube.com/watch?v=IJOn...

You can run Nufold at Google Colab:
colab.research.google.com/github/kihar...
Paper: www.nature.com/articles/s41...
Junior CASP: Yuki Kagaya Flash Talks
YouTube video by CASP
www.youtube.com
kiharalab.bsky.social
Our cryo-EM modeling tools are also available via
SBGrid. Here is a new tutorial video on DeepMainmast protein modeling and DAQ structure validation score presented at SBGrid Webinar:
youtu.be/z2ep8HilF-c
DeepMainmast and DAQ
YouTube video by SBGrid Consortium
youtu.be
kiharalab.bsky.social
New video tutorial for DAQ score for validating protein structures built from cryo-EM maps. Unique in identifying incorrectly assigned residues. Check it out now!

www.youtube.com/watch?v=YRAT...

Webserver: em.kiharalab.org/algorithm/da...
DAQ-Score: Automatic AI-based Cryo-EM Structure Model Validation!
YouTube video by Kihara Bioinformatics Lab
www.youtube.com
kiharalab.bsky.social
New paper by many people in our lab led by Charles Christoffer and Yuki Kagaya. This is an invited paper for the CAPRI protein docking special issue on Proteins: "Integrative Protein Assembly With LZerD and Deep Learning in CAPRI 47–55"
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Kihara Laboratory
iscb.bsky.social
#GLBIO2025 is accepting late-breaking poster abstract submissions!

If you missed the initial deadline, this is your chance to present your research and engage with the bioinformatics and computational biology community.

📥Submit now: https://t.ly/ByJrY
Reposted by Kihara Laboratory
Reposted by Kihara Laboratory
kiharalab.bsky.social
Hello Blue Sky! from Kiharalab, Purdue