This week Jacob successfully defended his PhD. Congratulations Dr. Verburgt!!

In the past few days, we noticed slowdown in our website, kiharalab.org due to ~1M/day of accesses being made to DAQ-DB from major IT companies bot and via unique IPs. Note that a full ZIP archive of DAQ-DB is available for download daqdb.kiharalab.org/download

New book chapter online: Translating a GO Term List to Human Readable Function Description Using GO2Sum by Swagarika Jaharlal Giri Udayan Pandey, joonhongpark & Daisuke Kihara Methods in Mol. Biol. The server is available kiharalab.org/go2sum_server/ link.springer.com/protocol/10.10…

CASP protein structure competition nears end as NIH grant money runs out | Science | AAAS science.org/content/articl…

ついにCASP終わるか。意外とCAPRIが生き残るとか。Exclusive: Famed protein structure competition nears end as NIH grant money runs out | Science | AAAS science.org/content/articl…

Joon Hong Park from Purdue Computer Science at American Crystallographic Association (ACA) 2025 meeting. presenting his poster about our cryo-EM structure modeling server. Visit the server for easy and accurate modeling at em.kiharalab.org

予算を得られたので、うちの研究室でポスドクの募集を開始します。深層学習を使ってタンパク質や核酸の立体構造予測（Alphafoldなどの関連ソフトのコードの理解を元に）や、電子顕微鏡の低解像度の画像からの構造モデリングが主なプロジェクトです。続）

New paper accepted: "Structure Modeling Protocols for Protein Multimer and RNA in CASP16 with Enhanced MSAs, Model Ranking, and Deep Learning" Yuki Kagaya et al., Proteins. This reports our strategies in CASP. The initial submission available at ggnpreprints.authorea.com/doi/full/10.22…

M&M 2025 PTSA travel award頂きました。#MM2025

David Platt summarizing his summer research with us at the REU undergraduate symposium. Great job on an awesome presentation! Purdue Structural and Comp. Biology & Biophysics Purdue Biological Sciences Purdue Science

Had a group lunch with summer interns with Jimmy John’s sandwiches 🥪

I will present DMcloud: Macromolecular Structure Modeling with Local Structure Fitting for Medium to Low Resolution Cryo-EM Maps In M&M2025 today, 2:45 PM – 3:00 PM. Please come to Room 251A!

A new book on Protein Function Prediction from Methods in Molecular Biology series edited by Daisuke Kihara & Lukasz Kurgan is now available! It includes 20 chapters on state-of-the-art computational protein function prediction methods and resources. link.springer.com/book/10.1007/9…

Our collaborative paper is available on bioRxiv. Divergence of an extracellular contractile injection system infectivity elucidated by high resolution structural studies of its tail-baseplate complex biorxiv.org/content/10.110…

2025 MSA Professional Technical Staff Awards (PTSA) academic.oup.com/mt/article-abs…

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

AlphaFold model quality self-assessment improvement via deep graph learning 1. Introducing EQAFold, an enhanced framework that refines the Local Distance Difference Test (LDDT) prediction head of AlphaFold to generate more accurate self-confidence scores for protein structure

Thank you for coming to the DAQ and DAQ-Refine cryo-EM structure validation workshop hosted by Purdue Structural Biology and Biophysics Club ! For those who missed it, we have Youtube video: youtube.com/watch?v=YRAT98… The presented tools are available at 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. Communications Biology nature.com/articles/s4200…

新しい論文のリリースです。アミノ酸残基の距離情報を考慮してAlphafoldの構造モデルを修正するDistance-AF. 新しく距離制約を学習したネットワークを作るのではなく、距離制約のロスの項を足してオーバーフィッティングを行います。Communications Biology.