kazuyoshi ikeda
kazuyoshi ikeda
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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
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
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
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
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
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
Assessing the druggability of protein-protein interactions by a supervised machine-learning method
N Sugaya, K Ikeda
BMC bioinformatics 10, 1-13, 2009
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
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
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
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
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
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
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
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
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
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
Measurement of pressure distribution on dies in porthole die extrusion
YT Kim, K Ikeda, T Murakami
Keikinzoku 49 (7), 296-301, 1999
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
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
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