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2020 – today
- 2024
[j30]Keisuke Yanagisawa
, Takuya Fujie, Kazuki Takabatake, Yutaka Akiyama:
QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. Entropy 26(5): 397 (2024)- [c27]Taisuke Boku, Masatake Sugita, Ryohei Kobayashi, Shinnosuke Furuya, Takuya Fujie, Masahito Ohue, Yutaka Akiyama:
Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization. ICPP 2024: 1082-1091 - 2023
- [j29]Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama:
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. J. Chem. Inf. Model. 63(7): 2240-2250 (2023) - 2022
- [j28]Jianan Li, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama:
Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning. Bioinform. 38(4): 1110-1117 (2022) - [j27]Kazuki Takabatake, Keisuke Yanagisawa, Yutaka Akiyama:
Solving Generalized Polyomino Puzzles Using the Ising Model. Entropy 24(3): 354 (2022) - [j26]Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama:
Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. J. Chem. Inf. Model. 62(18): 4549-4560 (2022) - 2021
- [j25]Masatake Sugita, Satoshi Sugiyama, Takuya Fujie, Yasushi Yoshikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama:
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. J. Chem. Inf. Model. 61(7): 3681-3695 (2021) - [i4]Masahito Ohue, Yutaka Akiyama:
MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions. CoRR abs/2105.03617 (2021) - 2020
- [j24]Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Masahito Ohue, Yutaka Akiyama:
Development of Computational Pipeline Software for Genome/Exome Analysis on the K Computer. Supercomput. Front. Innov. 7(1): 37-54 (2020) - [c26]Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama:
Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations. SCFA 2020: 23-39 - [i3]Masahito Ohue, Kento Aoyama, Yutaka Akiyama:
High-performance cloud computing for exhaustive protein-protein docking. CoRR abs/2006.08905 (2020)
2010 – 2019
- 2019
- [c25]Masahito Ohue, Marina Yamasawa, Kazuki Izawa, Yutaka Akiyama:
Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN. BIBE 2019: 152-156 - [c24]Keren Jiang, Di Zhang, Tsubasa Iino, Risa Kimura, Tatsuo Nakajima, Kana Shimizu, Masahito Ohue, Yutaka Akiyama:
A playful tool for predicting protein-protein docking. MUM 2019: 40:1-40:5 - [i2]Masahito Ohue, Ryota Ii, Keisuke Yanagisawa, Yutaka Akiyama:
Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph. CoRR abs/1907.01103 (2019) - 2018
- [j23]Shogo D. Suzuki, Masahito Ohue, Yutaka Akiyama:
PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM. Artif. Life Robotics 23(2): 205-212 (2018) - [j22]Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama:
MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. BMC Bioinform. 19-S(4): 61-72 (2018) - [j21]Takashi Tajimi, Naoki Wakui, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama:
Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. BMC Bioinform. 19-S(19): 157-170 (2018) - [j20]Tomohiro Ban, Masahito Ohue, Yutaka Akiyama:
Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem. Comput. Biol. Chem. 73: 139-146 (2018) - [j19]Keisuke Yanagisawa, Shunta Komine, Rikuto Kubota, Masahito Ohue, Yutaka Akiyama:
Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm. Comput. Biol. Chem. 74: 399-406 (2018) - 2017
- [j18]Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama:
Spresso: an ultrafast compound pre-screening method based on compound decomposition. Bioinform. 33(23): 3836-3843 (2017) - [c23]Tomohiro Ban, Masahito Ohue, Yutaka Akiyama:
Efficient hyperparameter optimization by using Bayesian optimization for drug-target interaction prediction. ICCABS 2017: 1-6 - [c22]Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama:
Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. ICIC (2) 2017: 549-558 - [i1]Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama:
Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. CoRR abs/1705.01667 (2017) - 2015
- [j17]Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama:
Faster sequence homology searches by clustering subsequences. Bioinform. 31(8): 1183-1190 (2015) - [j16]Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama:
Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures. BMC Syst. Biol. 9(S-1): S6 (2015) - 2014
- [j15]Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama:
MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinform. 30(22): 3281-3283 (2014) - [j14]Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa:
CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinform. 15: 406 (2014) - [j13]Satoshi Matsuoka, Hitoshi Sato, Osamu Tatebe, Michihiro Koibuchi, Ikki Fujiwara, Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama, Toyotaro Suzumura, Koji Ueno, Hiroki Kanezashi, Takemasa Miyoshi:
Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year. Supercomput. Front. Innov. 1(2): 89-107 (2014) - [c21]Yuki Komatsu, Takashi Ishida, Yutaka Akiyama:
Metagenomic Phylogenetic Classification Using Improved Naïve Bayes. ICIC (3) 2014: 262-270 - 2013
- [j12]Youhei Namiki, Takashi Ishida, Yutaka Akiyama:
Acceleration of sequence clustering using longest common subsequence filtering. BMC Bioinform. 14(S-8): S7 (2013) - [j11]Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama:
MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments. Source Code Biol. Medicine 8: 18 (2013) - [c20]Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama:
Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking. BCB 2013: 666 - [c19]Takehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama:
The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments. BCB 2013: 667 - [c18]Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama:
MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs. BCB 2013: 883 - 2012
- [c17]Youhei Namiki, Takashi Ishida, Yutaka Akiyama:
Fast DNA Sequence Clustering Based on Longest Common Subsequence. ICIC (3) 2012: 453-460 - [c16]Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama:
Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis. PRIB 2012: 178-187 - [c15]Shuji Suzuki, Takashi Ishida, Yutaka Akiyama:
An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers. SC Companion 2012: 1549-1550 - 2011
- [c14]Katsuya Kikuchi, Chihiro Ueda, Fumiaki Fujii, Yutaka Akiyama, Naoya Watanabe, Yasuhiro Kitamura, Toshio Gomyo, Toshikazu Okubo, Tetsuya Koyama, Tadashi Kamada, Masahiro Aoyagi, Kanji Otsuka:
PDN impedance analysis of TSV-decoupling capacitor embedded Silicon interposer for 3D-integrated CMOS image sensor system. 3DIC 2011: 1-4 - 2010
- [c13]Wisnu Ananta Kusuma, Yutaka Akiyama:
Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes. PDPTA 2010: 104-108
2000 – 2009
- 2009
- [j10]Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama:
In silico Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis. J. Bioinform. Comput. Biol. 7(6): 991-1012 (2009) - 2008
- [j9]Daisuke Tominaga, Fukumi Iguchi, Katsuhisa Horimoto, Yutaka Akiyama:
High-throughput Automated Image Processing System for Cell Array Observations. Inf. Media Technol. 3(1): 71-78 (2008) - [j8]Masakazu Sekijima, Junta Doi, Shinya Honda, Tamotsu Noguchi, Shigenori Shimizu, Yutaka Akiyama:
Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation. Inf. Media Technol. 3(1): 201-210 (2008) - [j7]Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama:
Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins. J. Bioinform. Comput. Biol. 6(6): 1133-1156 (2008) - 2007
- [c12]Akira Nukada, Yuichiro Hourai, Akira Nishida, Yutaka Akiyama:
High Performance 3D Convolution for Protein Docking on IBM Blue Gene. ISPA 2007: 958-969 - [c11]Masakazu Sekijima, Junta Doi, Tamotsu Noguchi, Yutaka Akiyama, Shigenori Shimizu:
Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L. Parallel and Distributed Computing and Networks 2007: 242-247 - 2004
- [j6]Kentaro Tomii, Yutaka Akiyama:
FORTE: a profile-profile comparison tool for protein fold recognition. Bioinform. 20(4): 594-595 (2004) - [j5]Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama:
Optimizing substitution matrices by separating score distributions. Bioinform. 20(6): 863-873 (2004) - 2003
- [j4]Tamotsu Noguchi, Yutaka Akiyama:
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res. 31(1): 492-493 (2003) - [c10]Ayuta Yamada, Hitoshi Tsunashima, Yoshinori Arai, Toru Ishizuka, Yutaka Akiyama:
Generation of 3D solid model from 3DX multi image micro CT (methods and application). CARS 2003: 1224-1229 - [c9]Daisuke Tominaga, Katsutoshi Takahashi, Yutaka Akiyama:
Distributed Genetic Algorithm for Inference of Biological Scale-Free Network Structure. ISHPC 2003: 214-221 - [c8]Masakazu Sekijima, Chie Motono, Satoshi Yamasaki, Kiyotoshi Kaneko, Yutaka Akiyama:
Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing. ISHPC 2003: 476-485 - 2002
- [j3]Kentaro Onizuka, Tamotsu Noguchi, Yutaka Akiyama, Hideo Matsuda:
Using Data Compression for Multidimensional Distribution Analysis. IEEE Intell. Syst. 17(3): 48-54 (2002) - 2001
- [j2]Tamotsu Noguchi, Hideo Matsuda, Yutaka Akiyama:
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). Nucleic Acids Res. 29(1): 219-220 (2001) - 2000
- [j1]Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama:
Quick selection of representative protein chain sets based on customizable requirements. Bioinform. 16(6): 520-526 (2000) - [c7]Makoto Ando, Yutaka Akiyama, Hideo Matsuda:
Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. PDPTA 2000
1990 – 1999
- 1999
- [c6]Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi, Makoto Ando:
Biological- and Chemical- Parallel Applications on a PC Cluster. ISHPC 1999: 220-233 - [c5]Makoto Ando, Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi:
ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides. PDPTA 1999: 1537-1543 - 1997
- [c4]Yutaka Akiyama, Kiyotaka Misoo, Yoshiharu Omura, Hiroshi Matsumoto, Minoru Saito, Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando:
Parallelization of Space Plasma Particle Simulation. ISHPC 1997: 281-292 - [c3]Kentaro Onizuka, Tamotsu Noguchi, Minoru Saito, Yutaka Akiyama:
Parallel PDB Data Retriever "PDB Diving Booster". ISHPC 1997: 389-396 - [c2]Tamotsu Noguchi, Kentaro Onizuka, Yutaka Akiyama, Minoru Saito:
PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank). ISMB 1997: 214-217
1980 – 1989
- 1989
- [c1]Masahiro Kajiura, Yutaka Akiyama, Yuichiro Anzai:
Solving large scale puzzles with neural networks. TAI 1989: 562-569
Coauthor Index
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