Kihara, Daisuke

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods

Bioinformatics and Genomic NetworksMachine Learning in Bioinformatics

Cited by 1,028

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 452

Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

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

Kagaya, Y., Zhang, Z., Ibtehaz, N., Wang, X., Nakamura, T., Punuru, P. D., & Kihara, D. (2025) · Nature Communications

RNA and protein synthesis mechanismsProtein Structure and Dynamics

Cited by 70

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

Aderinwale, T., Bharadwaj, V., Christoffer, C., Terashi, G., Zhang, Z., Jahandideh, R., Kagaya, Y., & Kihara, D. (2022) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 61

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

Aderinwale, T., Bharadwaj, V., Christoffer, C., Terashi, G., Zhang, Z., Jahandideh, R., Kagaya, Y., & Kihara, D. (2021) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 61

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

Zhang, Y., Zhang, Z., Kagaya, Y., Terashi, G., Zhao, B., Xiong, Y., & Kihara, D. (2023) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 20

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

Zhang, Y., Zhang, Z., Kagaya, Y., Terashi, G., Zhao, B., Xiong, Y., & Kihara, D. (2025) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 19

AlphaFold Model Quality Self-Assessment Improvement Via Deep Graph Learning

Verburgt, J., Zhang, Z., & Kihara, D. (2024) · Protein Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 8

AlphaFold model quality self‐assessment improvement via deep graph learning

Verburgt, J., Zhang, Z., & Kihara, D. (2025) · Protein Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 8

Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints

Christoffer, C., Harini, K., Archit, G., & Kihara, D. (2024) · Journal of Molecular Biology

Protein Structure and DynamicsLipid Membrane Structure and Behavior

Cited by 4

Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints

Christoffer, C., Harini, K., Archit, G., & Kihara, D. (2023) · Journal of Molecular Biology

Protein Structure and DynamicsLipid Membrane Structure and Behavior

Cited by 4

PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors

Shin, W.-H., Kagaya, Y., Jang, W., & Kihara, D. (2026) · Journal of Cheminformatics

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 3