| Community-wide assessment of protein-interface modeling suggests improvements to design methodology SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Journal of molecular biology 414 (2), 289-302, 2011 | 156 | 2011 |
| MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers M Ohue, T Shimoda, S Suzuki, Y Matsuzaki, T Ishida, Y Akiyama Bioinformatics 30 (22), 3281-3283, 2014 | 102 | 2014 |
| MEGADOCK: An All-to-all Protein-protein Interaction Prediction System Using Tertiary Structure Data M Ohue, Y Matsuzaki, N Uchikoga, T Ishida, Y Akiyama Protein and peptide letters 21 (8), 766-778, 2014 | 83 | 2014 |
| Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations M Sugita, S Sugiyama, T Fujie, Y Yoshikawa, K Yanagisawa, M Ohue, ... Journal of chemical information and modeling 61 (7), 3681-3695, 2021 | 50 | 2021 |
| Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem T Ban, M Ohue, Y Akiyama Computational biology and chemistry 73, 139-146, 2018 | 46 | 2018 |
| Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods M Ohue, Y Matsuzaki, T Shimoda, T Ishida, Y Akiyama BMC proceedings 7 (Suppl 7), S6, 2013 | 44 | 2013 |
| Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simulation approach N Wakui, R Yoshino, N Yasuo, M Ohue, M Sekijima Journal of Molecular Graphics and Modelling 79, 166-174, 2018 | 36 | 2018 |
| MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments Y Matsuzaki, N Uchikoga, M Ohue, T Shimoda, T Sato, T Ishida, ... Source code for biology and medicine 8, 1-8, 2013 | 32 | 2013 |
| MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions T Hayashi, Y Matsuzaki, K Yanagisawa, M Ohue, Y Akiyama BMC bioinformatics 19, 61-72, 2018 | 30 | 2018 |
| NRLMFβ: Beta-distribution-rescored neighborhood regularized logistic matrix factorization for improving the performance of drug–target interaction prediction T Ban, M Ohue, Y Akiyama Biochemistry and biophysics reports 18, 100615, 2019 | 27 | 2019 |
| Protein-protein Interaction Network Prediction by using Rigid-body Docking Tools: Application to Bacterial Chemotaxis Y Matsuzaki, M Ohue, N Uchikoga, Y Akiyama Protein and peptide letters 21 (8), 790-798, 2014 | 27 | 2014 |
| Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction T Ban, M Ohue, Y Akiyama Proceedings of the 7th IEEE International Conference on Computational …, 2017 | 23 | 2017 |
| Improvement of the protein–protein docking prediction by introducing a simple hydrophobic interaction model: an application to interaction pathway analysis M Ohue, Y Matsuzaki, T Ishida, Y Akiyama Pattern Recognition in Bioinformatics: 7th IAPR International Conference …, 2012 | 23 | 2012 |
| Quantitative estimate index for early-stage screening of compounds targeting protein-protein interactions T Kosugi, M Ohue International Journal of Molecular Sciences 22 (20), 10925, 2021 | 19 | 2021 |
| 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 | 19 | 2019 |
| The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency D Kami, T Kitani, A Nakamura, N Wakui, R Mizutani, M Ohue, F Kametani, ... PLoS One 13 (10), e0203708, 2018 | 17 | 2018 |
| QEX: target-specific druglikeness filter enhances ligand-based virtual screening M Mochizuki, SD Suzuki, K Yanagisawa, M Ohue, Y Akiyama Molecular Diversity 23, 11-18, 2019 | 16 | 2019 |
| Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures T Shimoda, S Suzuki, M Ohue, T Ishida, Y Akiyama BMC systems biology 9, 1-10, 2015 | 15 | 2015 |
| Structural basis for the binding mechanism of human serum albumin complexed with cyclic peptide dalbavancin S Ito, A Senoo, S Nagatoishi, M Ohue, M Yamamoto, K Tsumoto, N Wakui Journal of Medicinal Chemistry 63 (22), 14045-14053, 2020 | 13 | 2020 |
| Synthesis of triazolo-and oxadiazolopiperazines by gold (I)-catalyzed domino cyclization: Application to the design of a mitogen activated protein (MAP) kinase inhibitor K Yamamoto, Y Yoshikawa, M Ohue, S Inuki, H Ohno, S Oishi Organic letters 21 (2), 373-377, 2018 | 13 | 2018 |
Akiyama YutakaTokyo Institute of TechnologyVerified email at c.titech.ac.jp
