Kihara Laboratory
@kiharalab.bsky.social
Bioinformatics, protein modeling, cryoEM, drug screening, function prediction. Daisuke Kihara, professor of Biol/CS, Purdue U. https://kiharalab.org/ YouTube: http://alturl.com/gxvah
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/posts/distan...
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...
communities.springernature.com
November 7, 2025 at 3:54 PM
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/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....
We used DeepMainmast and DAQ for structure modeling.
pubs.acs.org/doi/full/10....
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...
pubs.acs.org
November 2, 2025 at 3:03 AM
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....
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
daqdb.kiharalab.org
Easy to use DAQ for structure validation in your paper: em.kiharalab.org
October 26, 2025 at 7:23 PM
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
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...
www.nature.com/articles/s42...
October 2, 2025 at 11:52 PM
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...
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/...
August 22, 2025 at 6:09 PM
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...
August 20, 2025 at 11:36 PM
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
The server: em.kiharalab.org
August 20, 2025 at 11:14 PM
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
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
August 19, 2025 at 10:14 PM
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
Visit the server for easy and accurate modeling at em.kiharalab.org
July 23, 2025 at 1:00 AM
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
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...
Paper: pubs.acs.org/doi/10.1021/...
Github: github.com/kiharalab/Di...
Google Colab: colab.research.google.com/drive/1Q1ecU...
June 21, 2025 at 4:59 PM
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...
Paper: pubs.acs.org/doi/10.1021/...
Github: github.com/kiharalab/Di...
Google Colab: colab.research.google.com/drive/1Q1ecU...
Reposted by Kihara Laboratory
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...
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…
www.nsf.gov
May 30, 2025 at 3:03 AM
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/...
pubs.acs.org
June 16, 2025 at 11:42 PM
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
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
May 30, 2025 at 12:17 AM
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
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...
www.nsf.gov/news/using-m...
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…
www.nsf.gov
May 7, 2025 at 4:43 PM
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...
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...
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
March 31, 2025 at 9:45 PM
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...
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
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
March 29, 2025 at 9:15 PM
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
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...
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
March 23, 2025 at 4:47 AM
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...
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/...
onlinelibrary.wiley.com/doi/10.1002/...
March 20, 2025 at 6:17 PM
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/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Kihara Laboratory
#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
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
March 5, 2025 at 12:30 PM
#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
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
Predict RNA tertiary structures using NuFold
February 8, 2025 at 8:04 PM
Predict RNA tertiary structures using NuFold
Reposted by Kihara Laboratory
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: 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.
www.science-tldr.com
February 25, 2025 at 6:33 PM
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.
Reposted by Kihara Laboratory
Revolutionary NuFold tool redefines RNA research, bridging decades-long gaps in medical discovery. Dive into the future of science.
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.
geekoo.news
February 25, 2025 at 10:00 AM
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...
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....
www.nature.com
March 4, 2025 at 10:52 PM
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
March 4, 2025 at 10:51 PM
Hello Blue Sky! from Kiharalab, Purdue