Yutaka Akiyama

Publication Activity (10 Years)

Years Active: 1989-2024
Publications (10 Years): 25

Top Topics

Molecular Dynamics

Minimum Cost Flow

Top Venues

J. Chem. Inf. Model.

Publications

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)
Keisuke Yanagisawa, Takuya Fujie, Kazuki Takabatake, Yutaka Akiyama
QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. Entropy 26 (5) (2024)
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) (2023)
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) (2022)
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) (2022)
Kazuki Takabatake, Keisuke Yanagisawa, Yutaka Akiyama
Solving Generalized Polyomino Puzzles Using the Ising Model. Entropy 24 (3) (2022)
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) (2021)
Masahito Ohue, Yutaka Akiyama
MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions. CoRR (2021)
Masahito Ohue, Kento Aoyama, Yutaka Akiyama
High-performance cloud computing for exhaustive protein-protein docking. CoRR (2020)
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) (2020)
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)
Masahito Ohue, Ryota Ii, Keisuke Yanagisawa, Yutaka Akiyama
Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph. CoRR (2019)
Masahito Ohue, Marina Yamasawa, Kazuki Izawa, Yutaka Akiyama
Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN. BIBE (2019)
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)
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. (4) (2018)
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 (2018)
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 (2018)
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) (2018)
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) (2018)
Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama
Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. ICIC (2) (2017)
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) (2017)
Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama
Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. CoRR (2017)
Tomohiro Ban, Masahito Ohue, Yutaka Akiyama
Efficient hyperparameter optimization by using Bayesian optimization for drug-target interaction prediction. ICCABS (2017)
Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama
Faster sequence homology searches by clustering subsequences. Bioinform. 31 (8) (2015)
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) (2015)
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) (2014)
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) (2014)
Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa
CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinform. 15 (2014)
Yuki Komatsu, Takashi Ishida, Yutaka Akiyama
Metagenomic Phylogenetic Classification Using Improved Naïve Bayes. ICIC (3) (2014)
Youhei Namiki, Takashi Ishida, Yutaka Akiyama
Acceleration of sequence clustering using longest common subsequence filtering. BMC Bioinform. 14 (S-8) (2013)
Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama
MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs. BCB (2013)
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 (2013)
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)
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)
Shuji Suzuki, Takashi Ishida, Yutaka Akiyama
An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers. SC Companion (2012)
Youhei Namiki, Takashi Ishida, Yutaka Akiyama
Fast DNA Sequence Clustering Based on Longest Common Subsequence. ICIC (3) (2012)
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)
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)
Wisnu Ananta Kusuma, Yutaka Akiyama
Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes. PDPTA (2010)
Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis. J. Bioinform. Comput. Biol. 7 (6) (2009)
Daisuke Tominaga, Fukumi Iguchi, Katsuhisa Horimoto, Yutaka Akiyama
High-throughput Automated Image Processing System for Cell Array Observations. Inf. Media Technol. 3 (1) (2008)
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) (2008)
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) (2008)
Masakazu Sekijima, Junta Doi, Tamotsu Noguchi, Yutaka Akiyama, S. Shimizu
Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L. Parallel and Distributed Computing and Networks (2007)
Akira Nukada, Yuichiro Hourai, Akira Nishida, Yutaka Akiyama
High Performance 3D Convolution for Protein Docking on IBM Blue Gene. ISPA (2007)
Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama
Optimizing substitution matrices by separating score distributions. Bioinform. 20 (6) (2004)
Kentaro Tomii, Yutaka Akiyama
FORTE: a profile-profile comparison tool for protein fold recognition. Bioinform. 20 (4) (2004)
Daisuke Tominaga, Katsutoshi Takahashi, Yutaka Akiyama
Distributed Genetic Algorithm for Inference of Biological Scale-Free Network Structure. ISHPC (2003)
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) (2003)
Masakazu Sekijima, Chie Motono, Satoshi Yamasaki, Kiyotoshi Kaneko, Yutaka Akiyama
Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing. ISHPC (2003)
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)
Kentaro Onizuka, Tamotsu Noguchi, Yutaka Akiyama, Hideo Matsuda
Using Data Compression for Multidimensional Distribution Analysis. IEEE Intell. Syst. 17 (3) (2002)
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) (2001)
Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama
Quick selection of representative protein chain sets based on customizable requirements. Bioinform. 16 (6) (2000)
Makoto Ando, Yutaka Akiyama, Hideo Matsuda
Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. PDPTA (2000)
Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi, Makoto Ando
Biological- and Chemical- Parallel Applications on a PC Cluster. ISHPC (1999)
Makoto Ando, Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi
ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides. PDPTA (1999)
Tamotsu Noguchi, Kentaro Onizuka, Yutaka Akiyama, Minoru Saito
PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank). ISMB (1997)
Kentaro Onizuka, Tamotsu Noguchi, Minoru Saito, Yutaka Akiyama
Parallel PDB Data Retriever "PDB Diving Booster". ISHPC (1997)
Yutaka Akiyama, Kiyotaka Misoo, Yoshiharu Omura, Hiroshi Matsumoto, Minoru Saito, Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando
Parallelization of Space Plasma Particle Simulation. ISHPC (1997)
Masahiro Kajiura, Yutaka Akiyama, Yuichiro Anzai
Solving large scale puzzles with neural networks. TAI (1989)