Yutaka Akiyama

Orcid: 0000-0003-2863-8703

According to our database1, Yutaka Akiyama authored at least 60 papers between 1989 and 2024.

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Bibliography

2024
QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking.
Entropy, May, 2024

Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization.
Proceedings of the 53rd International Conference on Parallel Processing, 2024

2023
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides.
J. Chem. Inf. Model., April, 2023

2022
Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations.
J. Chem. Inf. Model., 2022

Solving Generalized Polyomino Puzzles Using the Ising Model.
Entropy, 2022

Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning.
Bioinform., 2022

2021
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations.
J. Chem. Inf. Model., 2021

MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions.
CoRR, 2021

2020
Development of Computational Pipeline Software for Genome/Exome Analysis on the K Computer.
Supercomput. Front. Innov., 2020

High-performance cloud computing for exhaustive protein-protein docking.
CoRR, 2020

Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations.
Proceedings of the Supercomputing Frontiers - 6th Asian Conference, 2020

2019
Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph.
CoRR, 2019

A playful tool for predicting protein-protein docking.
Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia, 2019

Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN.
Proceedings of the 19th IEEE International Conference on Bioinformatics and Bioengineering, 2019

2018
Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm.
Comput. Biol. Chem., 2018

Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem.
Comput. Biol. Chem., 2018

Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques.
BMC Bioinform., 2018

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.
BMC Bioinform., 2018

PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM.
Artif. Life Robotics, 2018

2017
Spresso: an ultrafast compound pre-screening method based on compound decomposition.
Bioinform., 2017

Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach.
Proceedings of the Intelligent Computing Theories and Application, 2017

Efficient hyperparameter optimization by using Bayesian optimization for drug-target interaction prediction.
Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2017

2015
Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures.
BMC Syst. Biol., 2015

Faster sequence homology searches by clustering subsequences.
Bioinform., 2015

2014
Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year.
Supercomput. Front. Innov., 2014

CLAST: CUDA implemented large-scale alignment search tool.
BMC Bioinform., 2014

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.
Bioinform., 2014

Metagenomic Phylogenetic Classification Using Improved Naïve Bayes.
Proceedings of the Intelligent Computing in Bioinformatics - 10th International Conference, 2014

2013
MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.
Source Code Biol. Medicine, 2013

Acceleration of sequence clustering using longest common subsequence filtering.
BMC Bioinform., 2013

The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments.
Proceedings of the ACM Conference on Bioinformatics, 2013

MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs.
Proceedings of the ACM Conference on Bioinformatics, 2013

Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers.
Proceedings of the 2012 SC Companion: High Performance Computing, 2012

Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis.
Proceedings of the Pattern Recognition in Bioinformatics, 2012

Fast DNA Sequence Clustering Based on Longest Common Subsequence.
Proceedings of the Emerging Intelligent Computing Technology and Applications, 2012

2011
PDN impedance analysis of TSV-decoupling capacitor embedded Silicon interposer for 3D-integrated CMOS image sensor system.
Proceedings of the 2011 IEEE International 3D Systems Integration Conference (3DIC), Osaka, Japan, January 31, 2011

2010
Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2010

2009
<i>In silico</i> Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis.
J. Bioinform. Comput. Biol., 2009

2008
Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins.
J. Bioinform. Comput. Biol., 2008

High-throughput Automated Image Processing System for Cell Array Observations.
Inf. Media Technol., 2008

Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation.
Inf. Media Technol., 2008

2007
Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L.
Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Networks, 2007

High Performance 3D Convolution for Protein Docking on IBM Blue Gene.
Proceedings of the Parallel and Distributed Processing and Applications, 2007

2004
FORTE: a profile-profile comparison tool for protein fold recognition.
Bioinform., 2004

Optimizing substitution matrices by separating score distributions.
Bioinform., 2004

2003
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.
Nucleic Acids Res., 2003

Distributed Genetic Algorithm for Inference of Biological Scale-Free Network Structure.
Proceedings of the High Performance Computing, 5th International Symposium, 2003

Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing.
Proceedings of the High Performance Computing, 5th International Symposium, 2003

Generation of 3D solid model from 3DX multi image micro CT (methods and application).
Proceedings of the CARS 2003. Computer Assisted Radiology and Surgery. Proceedings of the 17th International Congress and Exhibition, 2003

2002
Using Data Compression for Multidimensional Distribution Analysis.
IEEE Intell. Syst., 2002

2001
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).
Nucleic Acids Res., 2001

2000
Quick selection of representative protein chain sets based on customizable requirements.
Bioinform., 2000

Hierarchical Approach to Parallel Tree Search for Protein Conformational Analysis.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2000

1999
ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 1999

Biological- and Chemical- Parallel Applications on a PC Cluster.
Proceedings of the High Performance Computing, Second International Symposium, 1999

1997
PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank).
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Parallel PDB Data Retriever "PDB Diving Booster".
Proceedings of the High Performance Computing, International Symposium, 1997

Parallelization of Space Plasma Particle Simulation.
Proceedings of the High Performance Computing, International Symposium, 1997

1989
Solving large scale puzzles with neural networks.
Proceedings of the IEEE International Workshop on Tools for Artificial Intelligence: Architectures, 1989


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