Yuki Kagaya

Biochemistry, Genetics and Molecular BiologyMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 2%percentile

4.5Author DataRank

Indexed papers

4in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 4 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Real-time structure search and structure classification for AlphaFold protein models

Communications Biology(2022)10.1038/s42003-022-03261-8

Top 11%

2.0DataRank

Top 11%63 citations

Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh +3 more

Papers

Driven by 25 papers — median percentile 76. Top paper: “Real-time structure search and structure classification for AlphaFold protein models”.

Real-time structure search and structure classification for AlphaFold protein models

Communications Biology(2022)10.1038/s42003-022-03261-8

Top 11%

2.0DataRank

Top 11%63 citations

Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh +3 more

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26609

Top 11%

1.9DataRank

Top 11%81 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation

Nature Communications(2025)10.1038/s41467-025-56261-7

N/A

0.598DataRank · unranked

53 citations

Zicong Zhang, Nabil Ibtehaz, Xiao Wang, Tsukasa Nakamura, Pranav Punuru +2 more

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Utrecht University Repository (Utrecht University)(2023)10.22541/au.168888815.53957253/v1

Top 36%

0.540DataRank

Top 36%17 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

Real-Time Structure Search and Structure Classification for AlphaFold Protein Models

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.21.465371

N/A

0DataRank · unranked

10 citations

Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh +3 more

ContactPFP: Protein Function Prediction Using Predicted Contact Information

Frontiers in Bioinformatics(2022)10.3389/fbinf.2022.896295

N/A

0DataRank · unranked

14 citations

Sean T. Flannery, Aashish Jain, Daisuke Kihara, Yuki Kagaya

Domain-PFP allows protein function prediction using function-aware domain embedding representations

Communications Biology(2023)10.1038/s42003-023-05476-9

N/A

0DataRank · unranked

35 citations

Yuki Kagaya, Daisuke Kihara, Nabil Ibtehaz

Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.01.569498

N/A

0DataRank · unranked

13 citations

Zicong Zhang, Yuki Kagaya, Genki Terashi, Bowen Zhao, Yi Xiong +2 more

NuFold: A Novel Tertiary RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center Representation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.20.558715

N/A

0DataRank · unranked

12 citations

Zicong Zhang, Nabil Ibtehaz, Xiao Wang, Tsukasa Nakamura, David Huang +2 more

Improved Peptide Docking with Privileged Knowledge Distillation using Deep Learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.01.569671

N/A

0DataRank · unranked

4 citations

Jacob Verburgt, Yuki Kagaya, Charles Christoffer, Daisuke Kihara, Zicong Zhang

Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.23.554486

N/A

0DataRank · unranked

0 citations

Yuki Kagaya, Daisuke Kihara, Nabil Ibtehaz

Genetic adaptation despite high gene flow in a range-expanding population

(2024)10.22541/au.172115088.83825068/v1

N/A

0DataRank · unranked

0 citations

Benjamin Daniels, William Hemstrom, Cataixa López, Yuki Kagaya, Daisuke Kihara +5 more

SHREC2024: Non-rigid Complementary Shapes Retrieval in Protein-protein Interactions

HAL (Le Centre pour la Communication Scientifique Directe)(2024)10.2312/3dor.20241173

Top 100%

0DataRank

Top 100%0 citations

Н А Зарубина, Camille Depenveiller, Nguyen, Hoang-Phuc, Vong, Vinh-Toan, M-T Tran +6 more

Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs , Model Ranking, and Deep Learning

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70033

N/A

0DataRank · unranked

6 citations

Tsukasa Nakamura, Jacob Verburgt, Anika Jain, Genki Terashi, Pranav Punuru +6 more

Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints

Communications Biology(2025)10.1038/s42003-025-08783-5

N/A

0DataRank · unranked

5 citations

Zicong Zhang, Yuki Kagaya, Genki Terashi, Bowen Zhao, Yi Xiong +2 more

Integrative Protein Assembly With LZerD and Deep Learning in CAPRI 47–55

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.26818

N/A

0DataRank · unranked

3 citations

Yuki Kagaya, Jacob Verburgt, Genki Terashi, Woong‐Hee Shin, Anika Jain +8 more

SHREC 2025: Protein surface shape retrieval including electrostatic potential

Computers & Graphics(2025)10.1016/j.cag.2025.104394

N/A

0DataRank · unranked

2 citations

Camille Depenveiller, Atsushi Tatsuma, Tin Barisin, Eugen Rusakov, Udo Göbel +23 more

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70079

N/A

0DataRank · unranked

1 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking

ACS Omega(2025)10.1021/acsomega.5c00967

N/A

0DataRank · unranked

2 citations

Jacob Verburgt, Yuki Kagaya, Charles Christoffer, Daisuke Kihara, Zicong Zhang

Structure Modeling Protocols for Protein Multimer and RNA in CASP16 with Enhanced MSAs, Model Ranking, and Deep Learning

(2025)10.22541/au.174478900.09405488/v1

N/A

0DataRank · unranked

0 citations

Tsukasa Nakamura, Jacob Verburgt, Anika Jain J, Genki Terashi, Pranav Punuru +6 more

Protein Contact Map Denoising Using Generative Adversarial Networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.26.174300

N/A

0DataRank · unranked

9 citations

Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara, Sai Raghavendra Maddhuri Venkata Subramaniya

Blind prediction of complex water and ion ensembles around RNA in CASP16

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.03.685595

N/A

0DataRank · unranked

0 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

AttentiveDist: Protein Inter-Residue Distance Prediction Using Deep Learning with Attention on Quadruple Multiple Sequence Alignments

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.24.396770

N/A

0DataRank · unranked

4 citations

Genki Terashi, Yuki Kagaya, Sai Raghavendra Maddhuri Venkata Subramaniya, Charles Christoffer, Daisuke Kihara +1 more

Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction

Scientific Reports(2021)10.1038/s41598-021-87204-z

N/A

0DataRank · unranked

27 citations

Genki Terashi, Yuki Kagaya, Sai Raghavendra Maddhuri Venkata Subramaniya, Charles Christoffer, Daisuke Kihara +1 more

Protein contact map refinement for improving structure prediction using generative adversarial networks

Bioinformatics(2021)10.1093/bioinformatics/btab220

N/A

0DataRank · unranked

13 citations

Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara, Sai Raghavendra Maddhuri Venkata Subramaniya

Yuki Kagaya

Indexed papers

Top data-sharing exemplar

Papers