Yuki Kagaya

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• On the state of protein function prediction: a report on the fourth CAFA challenge

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-11

• BPS2026 – NuFold and NuFold DB: Deep learning approach for RNA structure prediction and database of predicted structures

  Biophysical Journal · 2026-02-01

• Computational approaches for RNA structure prediction and design

  Cell Reports Physical Science · 2026-02-01

• Blind Prediction of Complex Water and Ion Ensembles Around <scp>RNA</scp> in <scp>CASP16</scp>

  Proteins Structure Function and Bioinformatics · 2025-11-08 · 1 citations

• Blind prediction of complex water and ion ensembles around RNA in CASP16Preprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-03

• 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;"

  2025-10-06

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

  Communications Biology · 2025-09-30 · 4 citations

• EMSuite Server: Advanced Tools for Cryo-EM Structure Modeling, Validation, and Refinement

  Structural Dynamics · 2025-09-01

• SHREC 2025: Protein surface shape retrieval including electrostatic potentialPreprint

  Computers & Graphics · 2025-08-27 · 2 citations

• 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 · 2025-08-01 · 6 citations

• Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking

  ACS Omega · 2025-06-16 · 2 citations

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

  2025-04-16

• Integrative Protein Assembly With <scp>LZerD</scp> and Deep Learning in <scp>CAPRI</scp> 47–55

  Proteins Structure Function and Bioinformatics · 2025-03-17 · 3 citations

• BPS2025 - Kihara Lab EM Webserver: A platform for automated cryo-EM structure analysis and modeling

  Biophysical Journal · 2025-02-01

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

  Nature Communications · 2025-01-21 · 51 citations

• Shrec 2025: Protein Surface Shape Retrieval Including Electrostatic PotentialPreprint

  SSRN Electronic Journal · 2025-01-01

• Genetic adaptation despite high gene flow in a range‐expanding population

  Molecular Ecology · 2024-08-31 · 10 citations

• Genetic adaptation despite high gene flow in a range-expanding populationPreprint

  2024-07-16