Yuki Kagaya

Purdue University West Lafayette — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

13h-index1.0kcitations50works2.72yr avg
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Research Topics

Protein Structure and Dynamics(18), Machine Learning in Bioinformatics(18), RNA and protein synthesis mechanisms(11), Enzyme Structure and Function(9), Bioinformatics and Genomic Networks(7)

Publications50 total

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta
2026Open Access
Computational approaches for RNA structure prediction and design
Cell Reports Physical Science·2026Open Access
BPS2026 – Unlocking cryo-EM structures: The EMSuite server for high-accuracy modeling and analysis
Biophysical Journal·2026
BPS2026 – NuFold and NuFold DB: Deep learning approach for RNA structure prediction and database of predicted structures
Biophysical Journal·2026
Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
Blind Prediction of Complex Water and Ion Ensembles Around <scp>RNA</scp> in <scp>CASP16</scp>
Proteins Structure Function and Bioinformatics·2025· 1 citedOpen Access
Blind prediction of complex water and ion ensembles around RNA in CASP16
2025Open Access
Author response for "Blind Prediction of Complex Water and Ion Ensembles Around &lt;scp&gt;RNA&lt;/scp&gt; in &lt;scp&gt;CASP16&lt;/scp&gt;"
2025
Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints
Communications Biology·2025Open Access
EMSuite Server: Advanced Tools for Cryo-EM Structure Modeling, Validation, and Refinement
Structural Dynamics·2025Open Access
SHREC 2025: Protein surface shape retrieval including electrostatic potential
Computers & Graphics·2025· 2 citedOpen Access
Structure Modeling Protocols for Protein Multimer and <scp>RNA</scp> in <scp>CASP16</scp> With Enhanced <scp>MSAs</scp> , Model Ranking, and Deep Learning
Proteins Structure Function and Bioinformatics·2025· 4 citedOpen Access
Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking
ACS Omega·2025· 2 citedOpen Access
Structure Modeling Protocols for Protein Multimer and RNA in CASP16 with Enhanced MSAs, Model Ranking, and Deep Learning
2025Open Access
Integrative Protein Assembly With <scp>LZerD</scp> and Deep Learning in <scp>CAPRI</scp> 47–55
Proteins Structure Function and Bioinformatics·2025· 3 citedOpen Access
BPS2025 - Kihara Lab EM Webserver: A platform for automated cryo-EM structure analysis and modeling
Biophysical Journal·2025
NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation
Nature Communications·2025· 42 citedOpen Access
Shrec 2025: Protein Surface Shape Retrieval Including Electrostatic Potential
SSRN Electronic Journal·2025Open Access
Genetic adaptation despite high gene flow in a range‐expanding population
Molecular Ecology·2024· 5 citedOpen Access
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Frequent Co-authors

Daisuke Kihara(35), Genki Terashi(22), Tsukasa Nakamura(10), Jacob Verburgt(10), Pranav Punuru(10), Charles Christoffer(9), Joon Hong Park(9), Kengo Kinoshita(8), Nabil Ibtehaz(8), Aashish Jain(7), Takeshi Obayashi(6), David Huang(6), Han Zhu(6), Yuichi Aoki(5), Sai Raghavendra Maddhuri Venkata Subramaniya(5), Emilia Tugolukova(5), Anindya Saha(5), Shu Li(5), Shu Tadaka(4), Yuanyuan Zhang(4)