| E-CELL: software environment for whole-cell simulation. M Tomita, K Hashimoto, K Takahashi, TS Shimizu, Y Matsuzaki, F Miyoshi, ... Bioinformatics (Oxford, England) 15 (1), 72-84, 1999 | 1089 | 1999 |
| 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: 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 |
| The E-CELL project: towards integrative simulation of cellular processes M Tomita, K Hashimoto, K Takahashi, Y Matsuzaki, R Matsushima, K Yugi, ... Proceedings of the fourth annual international conference on Computational …, 2000 | 51 | 2000 |
| 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, 1-10, 2013 | 44 | 2013 |
| In silico screening of protein–protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis Y Matsuzaki, Y Matsuzaki, T Sato, Y Akiyama Journal of bioinformatics and computational biology 7 (06), 991-1012, 2009 | 37 | 2009 |
| 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 |
| 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 |
| 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 |
| Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints N Uchikoga, Y Matsuzaki, M Ohue, T Hirokawa, Y Akiyama PLoS One 8 (7), e69365, 2013 | 10 | 2013 |
| Docking-calculation-based method for predicting protein-RNA interactions. M Ohue, Y Matsuzaki, Y Akiyama Genome Informatics. International Conference on Genome Informatics 25 (1), 25-39, 2011 | 10 | 2011 |
| Robust effects of Tsr–CheBp and CheA–CheYp affinity in bacterial chemotaxis Y Matsuzaki, S Kikuchi, M Tomita Artificial Intelligence in Medicine 41 (2), 145-150, 2007 | 6 | 2007 |
| MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data and its application to systems biology study M Ohue, Y Matsuzaki, Y Matsuzaki, T Sato, Y Akiyama IPSJ Transactions on Mathematical Modeling and its Applications 3 (3), 91-106, 2010 | 4 | 2010 |
| Improvement of all-to-all protein-protein interaction prediction system MEGADOCK M Ohue, Y Matsuzaki, Y Matsuzaki, Y Akiyama The 20th International Conference on Genome Informatics (GIW2009), 2009 | 3 | 2009 |
| Status of rock dynamics study in horonobe underground research laboratory, Japan T Sato, K Aoyagi, Y Matsuzaki, N Miyara, K Miyakawa Rock Dynamics and Applications 3, 575-580, 2018 | | 2018 |
| Article/Book Information M Ohue, T Shimoda, S Suzuki, Y Matsuzaki, T Ishida Bioinformatics 30 (22), 3281-3283, 2014 | | 2014 |
| A Model Library of Bacterial Chemotaxis on E‑Cell System Y Matsuzaki E-Cell System: Basic Concepts and Applications, 66-73, 2013 | | 2013 |
| Comparative study of bacterial chemotaxis models Y MATSUZAKI, M TOMITA IPSJ SIG Technical Reports 2005 (126), 5-8, 2005 | | 2005 |
| E-CELL: Towards Reconstruction of the Cell M Tomita, K Hashimoto, K Takahashi, Y Matsuzaki, R Matsushima, K Yugi, ... JOURNAL-JAPANESE SOCIETY FOR ARTIFICIAL INTELLIGENCE 15 (1), 21-26, 2000 | | 2000 |
| A Model Library of E. coli Chemotaxis on the E-Cell Simulation Environment Y Matsuzaki, TS Shimizu, M Tomita | | |
