| Antibody informatics for drug discovery H Shirai, C Prades, R Vita, P Marcatili, B Popovic, J Xu, JP Overington, ... Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844 (11), 2002-2015, 2014 | 85 | 2014 |
| Kotai Antibody Builder: automated high-resolution structural modeling of antibodies K Yamashita, K Ikeda, K Amada, S Liang, Y Tsuchiya, H Nakamura, ... Bioinformatics 30 (22), 3279-3280, 2014 | 64 | 2014 |
| High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations H Shirai, K Ikeda, K Yamashita, Y Tsuchiya, J Sarmiento, S Liang, ... Proteins: Structure, Function, and Bioinformatics 82 (8), 1624-1635, 2014 | 57 | 2014 |
| Free‐energy landscape of a chameleon sequence in explicit water and its inherent α/β bifacial property K Ikeda, J Higo Protein science 12 (11), 2542-2548, 2003 | 49 | 2003 |
| Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target S Chiba, K Ikeda, T Ishida, MM Gromiha, YH Taguchi, M Iwadate, ... Scientific reports 5 (1), 17209, 2015 | 46 | 2015 |
| Collation and data-mining of literature bioactivity data for drug discovery LJ Bellis, R Akhtar, B Al-Lazikani, F Atkinson, AP Bento, J Chambers, ... Biochemical Society Transactions 39 (5), 1365-1370, 2011 | 45 | 2011 |
| Assessing the druggability of protein-protein interactions by a supervised machine-learning method N Sugaya, K Ikeda BMC bioinformatics 10, 1-13, 2009 | 44 | 2009 |
| PoSSuM v. 2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs J Ito, K Ikeda, K Yamada, K Mizuguchi, K Tomii Nucleic acids research 43 (D1), D392-D398, 2015 | 37 | 2015 |
| An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes S Chiba, T Ishida, K Ikeda, M Mochizuki, R Teramoto, YH Taguchi, ... Scientific Reports 7 (1), 12038, 2017 | 33 | 2017 |
| Structural bases of GM1 gangliosidosis and Morquio B disease M Morita, S Saito, K Ikeda, K Ohno, K Sugawara, T Suzuki, T Togawa, ... Journal of human genetics 54 (9), 510-515, 2009 | 30 | 2009 |
| β‐Hairpins, α‐helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β‐hairpin of SH3 domain K Ikeda, OV Galzitskaya, H Nakamura, J Higo Journal of computational chemistry 24 (3), 310-318, 2003 | 30 | 2003 |
| EzCatDB: the enzyme reaction database, 2015 update N Nagano, N Nakayama, K Ikeda, M Fukuie, K Yokota, T Doi, T Kato, ... Nucleic acids research 43 (D1), D453-D458, 2015 | 28 | 2015 |
| An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data N Sugaya, K Ikeda, T Tashiro, S Takeda, J Otomo, Y Ishida, A Shiratori, ... BMC pharmacology 7, 1-15, 2007 | 25 | 2007 |
| A prospective compound screening contest identified broader inhibitors for Sirtuin 1 S Chiba, M Ohue, A Gryniukova, P Borysko, S Zozulya, N Yasuo, ... Scientific reports 9 (1), 19585, 2019 | 20 | 2019 |
| Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs K Ikeda, K Tomii, T Yokomizo, D Mitomo, K Maruyama, S Suzuki, J Higo Protein science 14 (5), 1253-1265, 2005 | 17 | 2005 |
| Identification of novel inhibitors of Keap1/Nrf2 by a promising method combining protein–protein interaction-oriented library and machine learning Y Shimizu, T Yonezawa, J Sakamoto, T Furuya, M Osawa, K Ikeda Scientific reports 11 (1), 7420, 2021 | 15 | 2021 |
| Transition state of a SH3 domain detected with principle component analysis and a charge‐neutralized all‐atom protein model D Mitomo, HK Nakamura, K Ikeda, A Yamagishi, J Higo PROTEINS: Structure, Function, and Bioinformatics 64 (4), 883-894, 2006 | 14 | 2006 |
| DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein–protein interactions K Ikeda, Y Maezawa, T Yonezawa, Y Shimizu, T Tashiro, S Kanai, ... Frontiers in Chemistry 10, 1090643, 2023 | 11 | 2023 |
| Miscellaneous topics in computer-aided drug design: synthetic accessibility and GPU computing, and other topics Y Fukunishi, T Mashimo, K Misoo, Y Wakabayashi, T Miyaki, S Ohta, ... Current Pharmaceutical Design 22 (23), 3555-3568, 2016 | 11 | 2016 |
| Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization K Matsumura, T Shimomura, Y Kubo, T Oka, N Kobayashi, S Imai, ... BMC Molecular and Cell Biology 22, 1-16, 2021 | 10 | 2021 |
