| Parallelization of MAFFT for large-scale multiple sequence alignments T Nakamura, KD Yamada, K Tomii, K Katoh Bioinformatics 34 (14), 2490-2492, 2018 | 849 | 2018 |
| Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 | 168 | 2016 |
| Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021 | 102 | 2021 |
| Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment MF Lensink, G Brysbaert, N Raouraoua, PA Bates, M Giulini, RV Honorato, ... Proteins: Structure, Function, and Bioinformatics 91 (12), 1658-1683, 2023 | 45 | 2023 |
| DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction G Terashi, X Wang, D Prasad, T Nakamura, D Kihara Nature Methods 21 (1), 122-131, 2024 | 29 | 2024 |
| Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment A Kryshtafovych, J Moult, WM Billings, D Della Corte, K Fidelis, S Kwon, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1987-1996, 2021 | 21 | 2021 |
| DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps T Nakamura, X Wang, G Terashi, D Kihara Nature methods 20 (6), 775-776, 2023 | 17 | 2023 |
| Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments T Nakamura, T Oda, Y Fukasawa, K Tomii Proteins: Structure, Function, and Bioinformatics 86, 274-282, 2018 | 13 | 2018 |
| NuFold: a novel tertiary RNA structure prediction method using deep learning with flexible nucleobase center representation Y Kagaya, Z Zhang, N Ibtehaz, X Wang, T Nakamura, D Huang, D Kihara bioRxiv, 2023 | 9 | 2023 |
| Protein ligand-binding site comparison by a reduced vector representation derived from multidimensional scaling of generalized description of binding sites T Nakamura, K Tomii Methods 93, 35-40, 2016 | 9 | 2016 |
| NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation Y Kagaya, Z Zhang, N Ibtehaz, X Wang, T Nakamura, PD Punuru, ... Nature communications 16 (1), 881, 2025 | 4 | 2025 |
| Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets T Nakamura, K Tomii Biophysics and Physicobiology 13, 139-147, 2016 | 3 | 2016 |
| Developing a novel recurrent neural network architecture with fewer parameters and good learning performance K D YAMADA, F Lin, T Nakamura Interdisciplinary information sciences 27 (1), 25-40, 2021 | 2 | 2021 |
| Protein Data Bank Japan: Computational resources for analysis of protein structures GJ Bekker, C Nagao, M Shirota, T Nakamura, T Katayama, D Kihara, ... Journal of Molecular Biology, 169013, 2025 | 1 | 2025 |
| AI-based quality assessment methods for protein structure models from Cryo-EM H Zhu, G Terashi, F Farheen, T Nakamura, D Kihara Current Research in Structural Biology, 100164, 2025 | 1 | 2025 |
| Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures GJ Bekker, C Nagao, M Shirota, T Nakamura, T Katayama, D Kihara, ... Protein Science 34 (3), e70052, 2025 | | 2025 |
| SHREC 2024: Non-rigid complementary shapes retrieval in protein-protein interactions T Yacoub, N Zarubina, C Depenveiller, HP Nguyen, VT Vong, MT Tran, ... 3DOR 2024: Eurographics Workshop on 3D Object Retrieval, 2024 | | 2024 |
| DAQ-score database and DAQ-refine: Deep-learning-based quality estimation and refinement of cryo-EM-derived protein models T Nakamura, X Wang, G Terashi, D Kihara Biophysical Journal 123 (3), 133a, 2024 | | 2024 |
| DeepMainmast and cryoREAD: Protein and DNA/RNA structure modeling for cryo-EM using deep learning G Terashi, X Wang, T Nakamura, D Kihara Biophysical Journal 123 (3), 133a, 2024 | | 2024 |
| Study of the Variability of the Native Protein Structure CW Christoffer, T Nakamura, X Han, WH Shin, G Terashi, L Monroe, ... Elsevier, 2024 | | 2024 |
