New paper:🧬 Queryome: A multi-agent AI system for biomedical literature analysis. Queryome is a deep research system with specialized LLM agents that orchestrate to a wide range of queries based on Pubmed citations. biorxiv.org/content/10.6... Try it: queryome.app

A quick tutorial on the DAQ structure validation score for protein models derived from cryo-EM. DAQ evaluates amino acid–level accuracy in your model. Consider including a DAQ validation report in your next publication! www.youtube.com/watch?v=YRAT...

December Update of DAQ-Score DB! Quality evaluations of protein models from cryo-EM. Now includes evaluation of 258,956 protein chains. Check at daqdb.kiharalab.org It's very easy to compute DAQ for your protein model. Add the validation result in your publication: em.kiharalab.org/algorithm/da...

Blog of our recent method, Distance-AF by the first author, Yuanyuan Zhang: "Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints". Original paper is published in Communications Biology. communities.springernature.com/posts/distan...

New paper in collaboration with Jinghui Luo lab at PSI Paul Scherrer Inst. "Structural Insights and Functional Dynamics of β-Lactoglobulin Fibrils", Nano Letters. We used DeepMainmast and DAQ for structure modeling. pubs.acs.org/doi/full/10....

October release of DAQ Score DB of cryo-EM str validation! Now includes 255,199 protein chains from 17,283 EMDB maps. Fig is an example with an entire helix having a residue shift. daqdb.kiharalab.org Easy to use DAQ for structure validation in your paper: em.kiharalab.org

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...

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/...

PNCC Cryo-EM modeling and validation workshop on Sep 3-5, 2025. Register now! tinyurl.com/Cryo-EMModel...

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

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

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

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...

NuFold, a new computational tool from the @kiharalab.bsky.social at @purduecs.bsky.social, accelerates 3D RNA structure and function discovery, opening new possibilities for faster development of RNA-based therapeutics and technologies. 🧪 www.nsf.gov/news/using-m...

New paper online: Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking | ACS Omega pubs.acs.org/doi/10.1021/...

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

Nufold RNA structure prediction method in NSF Stories: Using machine learning to speed up discovery for drug delivery and disease treatment www.nsf.gov/news/using-m...

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...

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

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...

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/...

#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

Predict RNA tertiary structures using NuFold

Discover NuFold, a groundbreaking tool for predicting 3D RNA structures, developed by Purdue University. It's set to transform RNA research and expedite drug development.

Revolutionary NuFold tool redefines RNA research, bridging decades-long gaps in medical discovery. Dive into the future of science.

New paper from our lab: "NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation", Nature Communications. www.nature.com/articles/s41...

Hello Blue Sky! from Kiharalab, Purdue