Takashi Ishida

Orcid: 0000-0002-9478-3223

Affiliations:
  • Tokyo Institute of Technology, Japan


According to our database1, Takashi Ishida authored at least 27 papers between 2007 and 2023.

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Bibliography

2023
Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets.
J. Chem. Inf. Model., November, 2023

Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs.
Frontiers Bioinform., May, 2023

2021
Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints.
J. Chem. Inf. Model., 2021

End-to-end learning for compound activity prediction based on binding pocket information.
BMC Bioinform., 2021

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

Sequence alignment using machine learning for accurate template-based protein structure prediction.
Bioinform., 2020

2019
End-to-End Learning Based Compound Activity Prediction Using Binding Pocket Information.
Proceedings of the Intelligent Computing Theories and Application, 2019

2018
Stacking Multiple Molecular Fingerprints for Improving Ligand-Based Virtual Screening.
Proceedings of the Intelligent Computing Theories and Application, 2018

Improvement of template-based protein structure prediction by using chimera alignment.
Proceedings of the 8th International Conference on Bioscience, 2018

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

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

D<sup>2</sup>P<sup>2</sup>: database of disordered protein predictions.
Nucleic Acids Res., 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

2009
PiSite: a database of protein interaction sites using multiple binding states in the PDB.
Nucleic Acids Res., 2009

2008
Prediction of disordered regions in proteins based on the meta approach.
Bioinform., 2008

2007
PrDOS: prediction of disordered protein regions from amino acid sequence.
Nucleic Acids Res., 2007


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