iiinova — where your digital self keeps evolving

Kihara Laboratory @kiharalab.bsky.social · 19/09/2026

The August update of DAQ-Score DB! It includes Cryo-EM protein model quality evaluations for 283,198 proteins. Figure is an example of a model with probable seq shifting error. daqdb.kiharalab.org DAQ is easy to compute for str validation for your paper: em.kiharalab.org/algorithm/da...

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Kihara Laboratory @kiharalab.bsky.social · 04/09/2026

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...

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Kihara Laboratory @kiharalab.bsky.social · 28/08/2026

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...

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Kihara Laboratory @kiharalab.bsky.social · 22/08/2026

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...

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Kihara Laboratory @kiharalab.bsky.social · 13/08/2026

📢 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

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Kihara Laboratory @kiharalab.bsky.social · 08/08/2026

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

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Kihara Laboratory @kiharalab.bsky.social · 05/08/2026

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!

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Kihara Laboratory @kiharalab.bsky.social · 18/07/2026

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/

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Kihara Laboratory @kiharalab.bsky.social · 11/07/2026

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.

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Kihara Laboratory @kiharalab.bsky.social · 10/07/2026

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...

youtube.com

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

YouTube video by Kihara Bioinformatics Lab

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Kihara Laboratory @kiharalab.bsky.social · 13/06/2026

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

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Kihara Laboratory @kiharalab.bsky.social · 31/05/2026

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!

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Kihara Laboratory @kiharalab.bsky.social · 16/05/2026

🚀 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...

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Reposted by Kihara Laboratory

Kihara Laboratory @kiharalab.bsky.social · 05/04/2026

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

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Kihara Laboratory @kiharalab.bsky.social · 30/04/2026

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!

Kihara Laboratory @kiharalab.bsky.social · 27/04/2026

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/...

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Kihara Laboratory @kiharalab.bsky.social · 05/04/2026

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

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Kihara Laboratory @kiharalab.bsky.social · 01/04/2026

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...

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Kihara Laboratory @kiharalab.bsky.social · 27/03/2026

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.

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Kihara Laboratory @kiharalab.bsky.social · 27/03/2026

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

kiharalab.org

Function Prediction Server

Predict protein functions using PFP, Phylo-PFP, ESG, and Domain-PFP, with GO2Sum functional summaries for your protein sequences.

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Kihara Laboratory @kiharalab.bsky.social · 24/03/2026

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...

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Reposted by Kihara Laboratory

Charles Bayly-Jones @charlesbj.bsky.social · 27/02/2026

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

Kihara Laboratory @kiharalab.bsky.social · 16/03/2026

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...

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Kihara Laboratory @kiharalab.bsky.social · 04/03/2026

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...

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Kihara Laboratory @kiharalab.bsky.social · 25/02/2026

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

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Reposted by Kihara Laboratory

AI x Bio Discovery @aixbiobot.bsky.social · 17/02/2026

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.

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Reposted by Kihara Laboratory

cryoEM papers @cryoempapers.bsky.social · 17/02/2026

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

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Kihara Laboratory @kiharalab.bsky.social · 14/02/2026

🧬 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...

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Reposted by Kihara Laboratory

Kihara Laboratory @kiharalab.bsky.social · 14/12/2025

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...

youtube.com

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

YouTube video by Kihara Bioinformatics Lab

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Kihara Laboratory @kiharalab.bsky.social · 01/02/2026

🚀 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...

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Kihara Laboratory @kiharalab.bsky.social · 16/01/2026

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

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Reposted by Kihara Laboratory

ChimeraX @chimerax.ucsf.edu · 16/01/2026

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...

PDB 7jsn colored by DAQ scores of fit in cryoEM map.

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Kihara Laboratory @kiharalab.bsky.social · 26/12/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 14/12/2025

youtube.com

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

YouTube video by Kihara Bioinformatics Lab

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Kihara Laboratory @kiharalab.bsky.social · 13/12/2025

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...

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Kihara Laboratory @kiharalab.bsky.social · 07/11/2025

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...

communities.springernature.com

Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints

Distance-AF is a computational method that enhances AlphaFold2 by integrating user-specified distance constraints, enabling accurate protein structures prediction on different applications. It demonst...

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Kihara Laboratory @kiharalab.bsky.social · 02/11/2025

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....

pubs.acs.org

Structural Insights and Functional Dynamics of β-Lactoglobulin Fibrils

Amyloid fibrils from β-lactoglobulin (β-LG), a major whey protein, have attracted interest for nanotechnology due to their biocompatibility, tunable surface chemistry, and ability to bind functional m...

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Kihara Laboratory @kiharalab.bsky.social · 26/10/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 03/10/2025

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...

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Kihara Laboratory @kiharalab.bsky.social · 22/08/2025

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/...

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Kihara Laboratory @kiharalab.bsky.social · 21/08/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 21/08/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 19/08/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 23/07/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 21/06/2025

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...

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Reposted by Kihara Laboratory

Emily R. Trunnell, Ph.D. @ertrunnell.bsky.social · 30/05/2025

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...

nsf.gov

Using machine learning to speed up discovery for drug delivery and disease treatment

A new computational tool developed with support from the U.S. National Science Foundation could greatly speed up determining the 3D structure of RNAs, a…

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Kihara Laboratory @kiharalab.bsky.social · 17/06/2025

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

pubs.acs.org

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Kihara Laboratory @kiharalab.bsky.social · 30/05/2025

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

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Kihara Laboratory @kiharalab.bsky.social · 31/03/2025

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...

youtube.com

Junior CASP: Yuki Kagaya Flash Talks

YouTube video by CASP

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