New preprint from our lab: PathFold, an AI framework that predicts protein-folding pathways directly from amino acid sequences. Beyond static str prediction, PathFold models intermediate states and the sequence of events along the folding pathway. www.biorxiv.org/content/10.6...

We posted a new preprint, Prot-LAMBDA. Unlike most protein language models, it is a pLM with an explicit encoding of protein structures. Strong performance in structure-related tasks including structure prediction. www.biorxiv.org/content/10.6...

New paper from our lab: "Queryome: orchestrating retrieval, reasoning, and synthesis across biomedical literature" Journal of Biomedical Semantics. Answers biological questions precisely with reference. State-of-the-art performance in multiple benchmarks. link.springer.com/article/10.1...

📢 New paper in Current Protocols! 🧬 We present practical protocols for ComplexModeler and CryoZeta, deep learning tools for modeling protein–DNA/RNA complexes from cryo-EM maps, freely available through EMSuite. 🔬💻 📄 doi.org/10.1002/cpz1... em.kiharalab.org

Pranav Punuru received the Best poster in Biology Award at the Microscopy & Microanalysis (M&M) conference at Milwaukee last week. Congratulations, Pranav! His poster was about the EM modeling server. em.kiharalab.org

The REU in Structural & Computational Biology Program at Purdue Structural Biology concluded last week with presentations at the Undergraduate Research Symposium. Pictured are Laura Dong and Isaiah Philip, whom we had the pleasure of hosting in our lab. They did a fantastic job!

New article "Comp. approaches for protein complex modeling for intermediate res. cryo-EM maps" in Progress in Mol Biol & Translational Sci, by Joon Hong Park, Terashi & Kihara. Introduces how to use DiffModeler and DMcloud in em.kiharalab.org pubmed.ncbi.nlm.nih.gov/42463252/

New paper by Nabil Ibtehaz presented at ACL2026: "Protein-STORY: Semantic Text-Oriented Representation Yields biologically meaningful Protein embeddings" aclanthology.org/2026.acl-sho... Aggregates diverse sci texts of protein's function, structure, evolution, etc into a single embedding.

In May (5/6 2026) we gave a webinar introducing our EM web server. The recording is now available! Highlighted 2 recent additions: • DAQplugin: On-the-fly structure validation for ChimeraX • CryoZeta: A heterogeneous str modeling for proteins and DNA/RNA www.youtube.com/watch?v=Aeyn...

KiharaLab cryo-EM Server Webinar - DAQplugin & CryoZeta (May 6, 2026)

YouTube video by Kihara Bioinformatics Lab

youtube.com

Presentations at the Hitchhiker's Guide Structural Biology symposium at Purdue last week! Anika, Farhanaz, Genki, Yuki with Professor Wah Chiu. hitchhikersguide2biogal.com

New group picture (May 2026)! We have openings for graduate students, postdocs, and other research positions. If you're interested in joining our team, feel free to reach out!

🚀 New paper in J Cheminformatics! "PL-PatchSurfer3: improved str-based virtual screening using 3D Zernike descriptors". Even in the deep learning era, this surface-based approach competes with modern DL methods, especially on apo & AlphaFold structures. link.springer.com/article/10.1...

We have a postdoc opening. Please check careers.iscb.org/jobs/view/9910

We will host a ~30-45 min webinar introducing EM-server for cryo-EM structure modeling on May 6 (Wed) 12:30pm (Eastern Time). Will introduce DAQ-Score plugin & CryoZeta. EM-Server: em.kiharalab.org Registration link: kiharalab-events.vercel.app Hope to see you there!

New collaboration paper with Bou-Abdallah lab just released! Multivalent recognition of ferritin by full-length NCOA4 enables robust ferritinophagy, Srivastava, Terashi et al., Protein Science onlinelibrary.wiley.com/doi/10.1002/...

We have a postdoc opening. Please check careers.iscb.org/jobs/view/9910

Our new book chapter has just been published! "Computational approaches for protein complex modeling for intermediate resolution cryo-EM maps" We introduced our recently developed tools available on the EM server (em.kiharalab.org). You can read it here: www.sciencedirect.com/science/chap...

Following our PFP server update, two more related tools: • NaviGO – explore & visualize GO term relationships kiharalab.org/navigo • Queryome – search protein function across genomes kiharalab.org/queryome Together with PFP, a full ecosystem for protein function analysis.

We’ve rebuilt our Protein Function Prediction (PFP) server from the ground up. New features: • Domain-PFP: self-supervised, domain-aware function prediction • GO2Sum: converts GO terms into UniProt-style functional summaries All methods (PFP, Phylo-PFP, ESG) now in one interface. kiharalab.org/pfp

Our review on peptide–protein docking is out in Chemical Communications. "Peptide-protein docking: from physics-based models to generative intelligence". We discuss the shift from physics-based docking to deep learning & generative models. pubs.rsc.org/en/content/a...

You should also try cryoZETA. It's quite impressive. em.kiharalab.org/algorithm/Cr...

The March update of DAQ-Score DB! Includes Cryo-EM protein model quality evaluations for 275,728 proteins. Now, we use a language model to interpret evaluation in text! 🔗 daqdb.kiharalab.org DAQ is easy to compute for structure validation in your paper: em.kiharalab.org/algorithm/da...

New collaboration paper with the Bou-Abdallah lab at SUNY Potsdam: "Ferritin iron uptake and oxidation are dynamically modulated by nucleotide phosphate architecture via electrostatic gating", International Journal of Biological Macromolecules. sciencedirect.com/science/arti...

Our presentations at Biophysical Society Meeting at San Francisco! On em.kiharalab.org by Joon Hong Park, em.kiharalab.org/algorithm/DM... by Genki Terashi, colab.research.google.com/github/kihar... by Yuki Kagaya. #bps2026

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta [new] expands modern structure prediction by integrating cryo-EM density and sequence info via a diffusion network for accurate de novo macromolecular modeling.

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta www.biorxiv.org/content/10.64898/2026.02.13.705846v1 #cryoEM

🧬 New review out in Cell Reports Physical Science! We survey the rapidly evolving landscape of RNA 3D structure prediction & design, from classical physics-based methods to cutting-edge deep learning, MSA-free models, and generative design. 👉 doi.org/10.1016/j.xc...

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...

DAQ-Score: Automatic AI-based Cryo-EM Structure Model Validation!

YouTube video by Kihara Bioinformatics Lab

youtube.com

🚀 First DAQ-Score DB update of 2026 is live! Cryo-EM protein model quality evaluations now cover 266,577 protein chains. 🔗 daqdb.kiharalab.org 🏁Check out also our New ChimeraX plugin! It lets you check DAQ scores during modeling! cxtoolshed.rbvi.ucsf.edu/apps/chimera...

DAQ score has now ChimeraX plugin! You can monitor DAQ interactively while modeling your proteins in an EM map on ChimeraX!

ChimeraX@chimerax.ucsf.edu · 8mo ago

The ChimeraX DAQplugin computes DAQ scores showing the agreement between atomic models and cryoEM maps. Available from ChimeraX menu Tools / More Tools. cxtoolshed.rbvi.ucsf.edu/apps/chimera...