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Akiyama Yutaka
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Fragment molecular orbital method: use of approximate electrostatic potential
T Nakano, T Kaminuma, T Sato, K Fukuzawa, Y Akiyama, M Uebayasi, ...
Chemical Physics Letters 351 (5-6), 475-480, 2002
4712002
Fragment molecular orbital method: application to polypeptides
T Nakano, T Kaminuma, T Sato, Y Akiyama, M Uebayasi, K Kitaura
Chemical Physics Letters 318 (6), 614-618, 2000
4082000
DBGET/LinkDB: an integrated database retrieval system
W Fujibuchi, S Goto, H Migimatsu, I Uchiyama, A Ogiwara, Y Akiyama, ...
Pac. Symp. Biocomput 98, 683-694, 1998
1681998
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
1562011
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
T Noguchi, Y Akiyama
Nucleic acids research 31 (1), 492-493, 2003
1072003
Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties
M Sekijima, C Motono, S Yamasaki, K Kaneko, Y Akiyama
Biophysical journal 85 (2), 1176-1185, 2003
1042003
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
1032014
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array
S Suzuki, M Kakuta, T Ishida, Y Akiyama
PloS one 9 (8), e103833, 2014
1012014
FORTE: a profile–profile comparison tool for protein fold recognition
K Tomii, Y Akiyama
Bioinformatics 20 (4), 594-595, 2004
982004
Structure of the N-terminal domain of PEX1 AAA-ATPase: characterization of a putative adaptor-binding domain
K Shiozawa, N Maita, K Tomii, A Seto, N Goda, Y Akiyama, T Shimizu, ...
Journal of Biological Chemistry 279 (48), 50060-50068, 2004
882004
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
832014
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)
T Noguchi, H Matsuda, Y Akiyama
Nucleic Acids Research 29 (1), 219-220, 2001
792001
Detecting outlying samples in microarray data: A critical assessment of the effect of outliers on sample classification
K Kadota, D Tominaga, Y Akiyama, K Takahashi
Chem-Bio Informatics Journal 3 (1), 30-45, 2003
622003
Functional restoration of bacteriomes and viromes by fecal microbiota transplantation
K Fujimoto, Y Kimura, JR Allegretti, M Yamamoto, Y Zhang, K Katayama, ...
Gastroenterology 160 (6), 2089-2102. e12, 2021
582021
Metagenome data on intestinal phage-bacteria associations aids the development of phage therapy against pathobionts
K Fujimoto, Y Kimura, M Shimohigoshi, T Satoh, S Sato, G Tremmel, ...
Cell host & microbe 28 (3), 380-389. e9, 2020
582020
Faster sequence homology searches by clustering subsequences
S Suzuki, M Kakuta, T Ishida, Y Akiyama
Bioinformatics 31 (8), 1183-1190, 2015
552015
In silico classification of major clearance pathways of drugs with their physiochemical parameters
M Kusama, K Toshimoto, K Maeda, Y Hirai, S Imai, K Chiba, Y Akiyama, ...
Drug Metabolism and Disposition 38 (8), 1362-1370, 2010
522010
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
512021
Parallel Protein Information Analysis (PAPIA) system running on a 64-node PC Cluster
Y Akiyama, K Onizuka, T Noguchi, M Ando
Genome Informatics 9, 131-140, 1998
471998
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
462018
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Articles 1–20