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D

Daisuke Kihara

purdue university

61H-index
466Paper Count
1.2WCitation Count
Published Papers 146
Publication Date
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Peptide–protein docking: from physics-based models to generative intelligence
errchem. commun.
IF0
err2026-04-03
err0
errOAAI
errKai Ling; Shu Li; Zicong Zhang; Woong-Hee Shin; Daisuke Kihara
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Ferritin iron uptake and oxidation are dynamically modulated by nucleotide phosphate architecture via electrostatic gating
errInternational Journal of Biological Macromolecules
IF8.5
err2026-02-26
err0
PREAI
errAnitha Rajendran; Sean Henley; Brent L. Nannenga; Genki Terashi; Ayush Srivastava; Daisuke Kihara; Fadi Bou-Abdallah
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errSave
Computational approaches for RNA structure prediction and design
errCell Reports Physical Science
IF7.3
err2026-02-09
err0
errOAAI
errYuki Kagaya; Boyuan Liu; Daisuke Kihara
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errSave
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16
errProteins: Structure, Function, and Bioinformatics
IF0
err2025-11-08
err0
PREAI
errRachael C. Kretsch; Elisa Posani; Eugene F. Baulin; Janusz M. Bujnicki; Giovanni Bussi; Thomas E. Cheatham III; Shi-Jie Chen; Arne Elofsson; Masoud Amiri Farsani; Olivia N. Fisher; M. Michael Gromiha; Ayush Gupta; Michiaki Hamada; K. Harini; Gang Hu; David Huang; Junichi Iwakiri; Anika Jain; Yuki Kagaya; Daisuke Kihara; Sebastian Kmiecik; Sowmya Ramaswamy Krishnan; Ikuo Kurisaki; Olivier Languin-Cattoën; Jun Li; Shanshan Li; Karim Malekzadeh; Tsukasa Nakamura; Wentao Ni; Chandran Nithin; Michael Z. Palo; Joon Hong Park; Smita P. Pilla; Simón Poblete; Fabrizio Pucci; Pranav Punuru; Anouka Saha; Kengo Sato; Ambuj Srivastava; Genki Terashi; Emilia Tugolukova; Jacob Verburgt; Qiqige Wuyun; Gül H. Zerze; Kaiming Zhang; Sicheng Zhang; Wei Zheng; Yuanzhe Zhou; Wah Chiu; David A. Case; Rhiju Das
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errSave
MVGFormer: Multi-view perspective with graph-guided transformer for cryo-ET segmentation
errKnowledge-Based Systems
IF7.6
err2025-11-06
err0
errOAAI
errHaoran Li; Xingjian Li; Huan Wang; Jiahua Shi; Huaming Chen; Yizhou Zhao; Bo Du; Johan Barthelemy; Daisuke Kihara; Jun Shen; Min Xu
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errSave
Proteomic analysis of metabolic adaptation in a unicellular cyanobacterium during light-dark cycles and nitrogen fixation
errScientific Reports
IF3.9
err2025-10-13
err0
errOAAI
errPunyatoya Panda; Swagarika J. Giri; Venkatesh P. Thirumalaikumar; Louis A. Sherman; Daisuke Kihara; Uma K. Aryal
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errSave
Structural Insights and Functional Dynamics of β-Lactoglobulin Fibrils
errNANO LETTERS
IF9.1
err2025-10-01
err0
PREAI
errSternke-Hoffmann, Rebecca; Rhyner, David; Terashi, Genki; Qureshi, Bilal Muhammad; Riek, Roland; Greenwald, Jason; Kihara, Daisuke; Lutz-Bueno, Viviane; Luo, Jinghui
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errSave
Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints
errCommunications Biology
IF5.1
err2025-09-30
err0
errOAAI
errYuanyuan Zhang; Zicong Zhang; Yuki Kagaya; Genki Terashi; Bowen Zhao; Yi Xiong; Daisuke Kihara
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errSave
SHREC 2025: Protein surface shape retrieval including electrostatic potential
errcomputers
IF0
err2025-08-27
err0
errOAAI
errTaher Yacoub; Camille Depenveiller; Atsushi Tatsuma; Tin Barisin; Eugen Rusakov; Udo Göbel; Yuxu Peng; Shiqiang Deng; Yuki Kagaya; Joon Hong Park; Daisuke Kihara; Marco Guerra; Giorgio Palmieri; Andrea Ranieri; Ulderico Fugacci; Silvia Biasotti; Ruiwen He; Halim Benhabiles; Adnane Cabani; Karim Hammoudi; Haotian Li; Hao Huang; Chunyan Li; Alireza Tehrani; Fanwang Meng; Farnaz Heidar-Zadeh; Tuan-Anh Yang; Matthieu Montes
errShare
errSave
AlphaFold model quality self-assessment improvement via deep graph learning
errProtein Science
IF5.2
err2025-08-18
err0
errOAAI
errJacob Verburgt; Zicong Zhang; Daisuke Kihara
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errSave
Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning
errproteins structure function and bioinformatics
IF0
err2025-08-01
err0
errOAAI
errYuki Kagaya; Tsukasa Nakamura; Jacob Verburgt; Anika Jain; Genki Terashi; Pranav Punuru; Emilia Tugolukova; Joon Hong Park; Anouka Saha; David Huang; Daisuke Kihara
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errSave
Dynamics of Sheath Subunit of a Contractile Injection System Studied at Atomic Level During Host Infection
errMicroscopy and Microanalysis
IF3
err2025-07-25
err0
errOAAI
errAnindito Sen; Tsukasa Nakamura; Genki Tarashi; Veer Bhatt; Kyungho Kim; Shankararaman Chellam; Le Tran; Daisuke Kihara
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errSave
DMcloud: Macromolecular Structure Modeling with Local Structure Fitting for Medium to Low Resolution Cryo-EM Maps
errMicroscopy and Microanalysis
IF3
err2025-07-25
err0
PREAI
errGenki Terashi; Xiao Wang; Yuanyuan Zhang; Han Zhu; Daisuke Kihara
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errSave
Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor
errNATURE
IF48.5
err2025-05-21
err0
PREAI
errChen, Qiuyan; Schafer, Christopher T.; Mukherjee, Somnath; Wang, Kai; Gustavsson, Martin; Fuller, James R.; Tepper, Katelyn; Lamme, Thomas D.; Aydin, Yasmin; Agrawal, Parth; Terashi, Genki; Yao, Xin-Qiu; Kihara, Daisuke; Kossiakoff, Anthony A.; Handel, Tracy M.
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Integrative Protein Assembly With LZerD and Deep Learning in CAPRI 47-55
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2025-03-01
err0
PREAI
errChristoffer, Charles; Kagaya, Yuki; Verburgt, Jacob; Terashi, Genki; Shin, Woong-Hee; Jain, Anika; Sarkar, Daipayan; Aderinwale, Tunde; Subramaniya, Sai Raghavendra Maddhuri Venkata; Wang, Xiao; Zhang, Zicong; Zhang, Yuanyuan; Kihara, Daisuke
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errSave
Advancing structure modeling from cryo-EM maps with deep learning
errBIOCHEMICAL SOCIETY TRANSACTIONS
IF4.3
err2025-02-07
err0
PREAI
errLi, Shu; Terashi, Genki; Zhang, Zicong; Kihara, Daisuke
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errSave
AI-based methods for biomolecular structure modeling for Cryo-EM
errCURRENT OPINION IN STRUCTURAL BIOLOGY
IF7
err2025-02-01
err2
PREAI
errFarheen, Farhanaz; Terashi, Genki; Zhu, Han; Kihara, Daisuke
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errSave
Proteomic Analysis of Unicellular Cyanobacterium Crocosphaera subtropica ATCC 51142 under Extended Light or Dark Growth
errJOURNAL OF PROTEOME RESEARCH
IF3.6
err2025-01-29
err0
errOAAI
errPanda, Punyatoya; Giri, Swagarika J.; Sherman, Louis A.; Kihara, Daisuke; Aryal, Uma K.
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errSave
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology
errGIGASCIENCE
IF3.9
err2025-01-01
err0
PREAI
errXu, Qibo; Wu, Leon; Rebelo, Michael; Feng, Shi; Yu, Xinye; Farheen, Farhanaz; Kihara, Daisuke; Zhou, Z. Hong
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errSave
DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model
errNATURE METHODS
IF32.1
err2024-10-21
err0
PREAI
errWang, Xiao; Zhu, Han; Terashi, Genki; Taluja, Manav; Kihara, Daisuke
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Research Directions

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Co-authors
Cooperation Journals
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陈豪 (Hao Chen)
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Zhiping Weng
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张扬 cover
张扬 (Yang Zhang)
H-index: 112 · Papers: 1.6K
L
Luigi Cavallo
H-index: 112 · Papers: 1.2K
S
S.K. Burley
H-index: 106 · Papers: 1.3K
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