Kihara Laboratory

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...

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…

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

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…

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...

YouTube video by CASP Junior CASP: Yuki Kagaya Flash Talks

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 video by SBGrid Consortium DeepMainmast and DAQ

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

YouTube video by Kihara Bioinformatics Lab DAQ-Score: Automatic AI-based Cryo-EM Structure Model Validation!

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

NuFold: Pioneering 3D RNA Structure Prediction at Purdue University 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.

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.

NuFold Unleashes New Era in RNA Structure Prediction Discover how Purdue's groundbreaking NuFold is revolutionizing RNA research and accelerating medical discoveries by decoding life's hidden structures.

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

NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation - Nature Communications The 3D structure of RNA is crucial for unraveling its functions. Here, the authors developed NuFold, an end-to-end deep learning-based approach that predicts all-atom RNA 3D structures from sequences....

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