Yutaka Akiyama

62 papers A 1B 2C 2Misc 3Journal 35Unranked 19

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations. J. Chem. Inf. Model. Kairi Furui, Takafumi Shimizu, Yutaka Akiyama, S. Roy Kimura, Yoh Terada, Masahito Ohue
2024	J	`jnl`	CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation. Briefings Bioinform. Jianan Li, Keisuke Yanagisawa, Yutaka Akiyama
2024	B	`conf`	Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization. ICPP Taisuke Boku, Masatake Sugita, Ryohei Kobayashi, Shinnosuke Furuya, Takuya Fujie, Masahito Ohue, Yutaka Akiyama
2024	J	`jnl`	QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. Entropy Keisuke Yanagisawa, Takuya Fujie, Kazuki Takabatake, Yutaka Akiyama
2023	J	`jnl`	CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. J. Chem. Inf. Model. Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama
2022	J	`jnl`	Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. J. Chem. Inf. Model. Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2022	J	`jnl`	Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning. Bioinform. Jianan Li, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama
2022	J	`jnl`	Solving Generalized Polyomino Puzzles Using the Ising Model. Entropy Kazuki Takabatake, Keisuke Yanagisawa, Yutaka Akiyama
2021	J	`jnl`	Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. J. Chem. Inf. Model. Masatake Sugita, Satoshi Sugiyama, Takuya Fujie, Yasushi Yoshikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2021	J	`jnl`	MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions. CoRR Masahito Ohue, Yutaka Akiyama
2020	J	`jnl`	Development of Computational Pipeline Software for Genome/Exome Analysis on the K Computer. Supercomput. Front. Innov. Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Masahito Ohue, Yutaka Akiyama
2020	J	`jnl`	High-performance cloud computing for exhaustive protein-protein docking. CoRR Masahito Ohue, Kento Aoyama, Yutaka Akiyama
2020	—	`conf`	Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations. SCFA Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama
2019	B	`conf`	A playful tool for predicting protein-protein docking. MUM Keren Jiang, Di Zhang, Tsubasa Iino, Risa Kimura, Tatsuo Nakajima, Kana Shimizu, Masahito Ohue, Yutaka Akiyama
2019	J	`jnl`	Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph. CoRR Masahito Ohue, Ryota Ii, Keisuke Yanagisawa, Yutaka Akiyama
2019	C	`conf`	Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN. BIBE Masahito Ohue, Marina Yamasawa, Kazuki Izawa, Yutaka Akiyama
2018	J	`jnl`	Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. BMC Bioinform. Takashi Tajimi, Naoki Wakui, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama
2018	J	`jnl`	MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. BMC Bioinform. Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2018	J	`jnl`	Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem. Comput. Biol. Chem. Tomohiro Ban, Masahito Ohue, Yutaka Akiyama
2018	J	`jnl`	Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm. Comput. Biol. Chem. Keisuke Yanagisawa, Shunta Komine, Rikuto Kubota, Masahito Ohue, Yutaka Akiyama
2018	J	`jnl`	PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM. Artif. Life Robotics Shogo D. Suzuki, Masahito Ohue, Yutaka Akiyama
2017	—	`conf`	Efficient hyperparameter optimization by using Bayesian optimization for drug-target interaction prediction. ICCABS Tomohiro Ban, Masahito Ohue, Yutaka Akiyama
2017	—	`conf`	Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. ICIC (2) Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama
2017	J	`jnl`	Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. CoRR Masahito Ohue, Takuro Yamazaki, Tomohiro Ban, Yutaka Akiyama
2017	J	`jnl`	Spresso: an ultrafast compound pre-screening method based on compound decomposition. Bioinform. Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
2015	J	`jnl`	Faster sequence homology searches by clustering subsequences. Bioinform. Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama
2015	J	`jnl`	Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures. BMC Syst. Biol. Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
2014	J	`jnl`	CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinform. Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa
2014	J	`jnl`	Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year. Supercomput. Front. Innov. 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
2014	J	`jnl`	MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinform. Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama
2014	—	`conf`	Metagenomic Phylogenetic Classification Using Improved Naïve Bayes. ICIC (3) Yuki Komatsu, Takashi Ishida, Yutaka Akiyama
2013	J	`jnl`	Acceleration of sequence clustering using longest common subsequence filtering. BMC Bioinform. Youhei Namiki, Takashi Ishida, Yutaka Akiyama
2013	—	`conf`	Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking. BCB Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama
2013	J	`jnl`	MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments. Source Code Biol. Medicine Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama
2013	—	`conf`	MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs. BCB Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama
2013	—	`conf`	The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments. BCB Takehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
2012	—	`conf`	An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers. SC Companion Shuji Suzuki, Takashi Ishida, Yutaka Akiyama
2012	—	`conf`	Fast DNA Sequence Clustering Based on Longest Common Subsequence. ICIC (3) Youhei Namiki, Takashi Ishida, Yutaka Akiyama
2012	—	`conf`	Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis. PRIB Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama
2011	—	`conf`	PDN impedance analysis of TSV-decoupling capacitor embedded Silicon interposer for 3D-integrated CMOS image sensor system. 3DIC Katsuya Kikuchi, Chihiro Ueda, Fumiaki Fujii, Yutaka Akiyama, Naoya Watanabe, Yasuhiro Kitamura, Toshio Gomyo, Toshikazu Okubo, Tetsuya Koyama, Tadashi Kamada, Masahiro Aoyagi, Kanji Otsuka
2010	Misc	`conf`	Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes. PDPTA Wisnu Ananta Kusuma, Yutaka Akiyama
2008	J	`jnl`	Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins. J. Bioinform. Comput. Biol. Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
2008	J	`jnl`	Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation. Inf. Media Technol. Masakazu Sekijima, Junta Doi, Shinya Honda, Tamotsu Noguchi, Shigenori Shimizu, Yutaka Akiyama
2008	J	`jnl`	High-throughput Automated Image Processing System for Cell Array Observations. Inf. Media Technol. Daisuke Tominaga, Fukumi Iguchi, Katsuhisa Horimoto, Yutaka Akiyama
2007	C	`conf`	High Performance 3D Convolution for Protein Docking on IBM Blue Gene. ISPA Akira Nukada, Yuichiro Hourai, Akira Nishida, Yutaka Akiyama
2007	—	`conf`	Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L. Parallel and Distributed Computing and Networks Masakazu Sekijima, Junta Doi, Tamotsu Noguchi, Yutaka Akiyama, Shigenori Shimizu
2004	J	`jnl`	FORTE: a profile-profile comparison tool for protein fold recognition. Bioinform. Kentaro Tomii, Yutaka Akiyama
2004	J	`jnl`	Optimizing substitution matrices by separating score distributions. Bioinform. Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama
2003	—	`conf`	Distributed Genetic Algorithm for Inference of Biological Scale-Free Network Structure. ISHPC Daisuke Tominaga, Katsutoshi Takahashi, Yutaka Akiyama
2003	—	`conf`	Generation of 3D solid model from 3DX multi image micro CT (methods and application). CARS Ayuta Yamada, Hitoshi Tsunashima, Yoshinori Arai, Toru Ishizuka, Yutaka Akiyama
2003	—	`conf`	Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing. ISHPC Masakazu Sekijima, Chie Motono, Satoshi Yamasaki, Kiyotoshi Kaneko, Yutaka Akiyama
2003	J	`jnl`	PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res. Tamotsu Noguchi, Yutaka Akiyama
2002	J	`jnl`	Using Data Compression for Multidimensional Distribution Analysis. IEEE Intell. Syst. Kentaro Onizuka, Tamotsu Noguchi, Yutaka Akiyama, Hideo Matsuda
2001	J	`jnl`	PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). Nucleic Acids Res. Tamotsu Noguchi, Hideo Matsuda, Yutaka Akiyama
2000	Misc	`conf`	Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis. PDPTA Makoto Ando, Yutaka Akiyama, Hideo Matsuda
2000	J	`jnl`	Quick selection of representative protein chain sets based on customizable requirements. Bioinform. Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama
1999	—	`conf`	Biological- and Chemical- Parallel Applications on a PC Cluster. ISHPC Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi, Makoto Ando
1999	Misc	`conf`	ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides. PDPTA Makoto Ando, Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi
1997	A	`conf`	PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank). ISMB Tamotsu Noguchi, Kentaro Onizuka, Yutaka Akiyama, Minoru Saito
1997	—	`conf`	Parallel PDB Data Retriever "PDB Diving Booster". ISHPC Kentaro Onizuka, Tamotsu Noguchi, Minoru Saito, Yutaka Akiyama
1997	—	`conf`	Parallelization of Space Plasma Particle Simulation. ISHPC Yutaka Akiyama, Kiyotaka Misoo, Yoshiharu Omura, Hiroshi Matsumoto, Minoru Saito, Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando
1989	—	`conf`	Solving large scale puzzles with neural networks. TAI Masahiro Kajiura, Yutaka Akiyama, Yuichiro Anzai