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Y

Yuki Kagaya

purdue university

13H-index
50Paper Count
1.0KCitation Count
Published Papers 16
Publication Date
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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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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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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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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
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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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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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Domain-PFP allows protein function prediction using function-aware domain embedding representations
errCOMMUNICATIONS BIOLOGY
IF5.1
err2023-10-31
err5
errOAAI
errIbtehaz, Nabil; Kagaya, Yuki; Kihara, Daisuke
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2023-10-31
err33
errOAAI
errLensink, Marc F.; Brysbaert, Guillaume; Raouraoua, Nessim; Bates, Paul A.; Giulini, Marco; Honorato, Rodrigo V.; van Noort, Charlotte; Teixeira, Joao M. C.; Bonvin, Alexandre M. J. J.; Kong, Ren; Shi, Hang; Lu, Xufeng; Chang, Shan; Liu, Jian; Guo, Zhiye; Chen, Xiao; Morehead, Alex; Roy, Raj S.; Wu, Tianqi; Giri, Nabin; Quadir, Farhan; Chen, Chen; Cheng, Jianlin; Del Carpio, Carlos A.; Ichiishi, Eichiro; Rodriguez-Lumbreras, Luis A.; Fernandez-Recio, Juan; Harmalkar, Ameya; Chu, Lee-Shin; Canner, Sam; Smanta, Rituparna; Gray, Jeffrey J.; Li, Hao; Lin, Peicong; He, Jiahua; Tao, Huanyu; Huang, Sheng-You; Roel-Touris, Jorge; Jimenez-Garcia, Brian; Christoffer, Charles W.; Jain, Anika J.; Kagaya, Yuki; Kannan, Harini; Nakamura, Tsukasa; Terashi, Genki; Verburgt, Jacob C.; Zhang, Yuanyuan; Zhang, Zicong; Fujuta, Hayato; Sekijima, Masakazu; Kihara, Daisuke; Khan, Omeir; Kotelnikov, Sergei; Ghani, Usman; Padhorny, Dzmitry; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima; Negi, Surendra S.; Ricciardelli, Tiziana; Barradas-Bautista, Didier; Cao, Zhen; Chawla, Mohit; Cavallo, Luigi; Oliva, Romina; Yin, Rui; Cheung, Melyssa; Guest, Johnathan D.; Lee, Jessica; Pierce, Brian G.; Shor, Ben; Cohen, Tomer; Halfon, Matan; Schneidman-Duhovny, Dina; Zhu, Shaowen; Yin, Rujie; Sun, Yuanfei; Shen, Yang; Maszota-Zieleniak, Martyna; Bojarski, Krzysztof K.; Lubecka, Emilia A.; Marcisz, Mateusz; Danielsson, Annemarie; Dziadek, Lukasz; Gaardlos, Margrethe; Gieldon, Artur; Liwo, Adam; Samsonov, Sergey A.; Slusarz, Rafal; Zieba, Karolina; Sieradzan, Adam K.; Czaplewski, Cezary; Kobayashi, Shinpei; Miyakawa, Yuta; Kiyota, Yasuomi; Takeda-Shitaka, Mayuko; Olechnovic, Kliment; Valancauskas, Lukas; Dapkunas, Justas; Venclovas, Ceslovas; Wallner, Bjorn; Yang, Lin; Hou, Chengyu; He, Xiaodong; Guo, Shuai; Jiang, Shenda; Ma, Xiaoliang; Duan, Rui; Qui, Liming; Xu, Xianjin; Zou, Xiaoqin; Velankar, Sameer; Wodak, Shoshana J.
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COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations
errNUCLEIC ACIDS RESEARCH
IF13.1
err2022-11-09
err13
errOAAI
errObayashi, Takeshi; Kodate, Shun; Hibara, Himiko; Kagaya, Yuki; Kinoshita, Kengo
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Real-time structure search and structure classification for AlphaFold protein models
errCOMMUNICATIONS BIOLOGY
IF5.1
err2022-04-05
err42
errOAAI
errAderinwale, Tunde; Bharadwaj, Vijay; Christoffer, Charles; Terashi, Genki; Zhang, Zicong; Jahandideh, Rashidedin; Kagaya, Yuki; Kihara, Daisuke
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ATTED-II v11: A Plant Gene Coexpression Database Using a Sample Balancing Technique by Subagging of Principal Components
errPLANT AND CELL PHYSIOLOGY
IF4
err2022-03-30
err59
errOAAI
errObayashi, Takeshi; Hibara, Himiko; Kagaya, Yuki; Aoki, Yuichi; Kinoshita, Kengo
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Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction
errSCIENTIFIC REPORTS
IF3.9
err2021-04-07
err20
errOAAI
errJain, Aashish; Terashi, Genki; Kagaya, Yuki; Subramaniya, Sai Raghavendra Maddhuri Venkata; Christoffer, Charles; Kihara, Daisuke
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MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2020-03-20
err10
errOAAI
errTerashi, Genki; Kagaya, Yuki; Kihara, Daisuke
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COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference
errNUCLEIC ACIDS RESEARCH
IF13.1
err2018-11-20
err114
errOAAI
errObayashi, Takeshi; Kagaya, Yuki; Aoki, Yuichi; Tadaka, Shu; Kinoshita, Kengo
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ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index (vol 59, pg E3, 2017)
errPLANT AND CELL PHYSIOLOGY
IF4
err2018-01-10
err39
errOAAI
errObayashi, Takeshi; Aoki, Yuichi; Tadaka, Shu; Kagaya, Yuki; Kinoshita, Kengo
errShare
errSave
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index
errPLANT AND CELL PHYSIOLOGY
IF4
err2017-12-04
err179
errOAAI
errObayashi, Takeshi; Aoki, Yuichi; Tadaka, Shu; Kagaya, Yuki; Kinoshita, Kengo
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Research Directions

No research directions
Co-authors
Cooperation Journals
L
Luigi Cavallo
H-index: 112 · Papers: 1.2K
D
David A. Case
H-index: 107 · Papers: 518
W
Wah Chiu
H-index: 105 · Papers: 819
A
Alexandre M. J. J. Bonvin
H-index: 82 · Papers: 506
S
Shoshana J. Wodak
H-index: 77 · Papers: 301
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