Daisuke Kihara

According to our database1, Daisuke Kihara authored at least 58 papers between 2006 and 2020.

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Bibliography

2020
Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes.
Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

2DKD: a toolkit for content-based local image search.
Source Code Biol. Medicine, 2020

MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.
J. Chem. Inf. Model., 2020

SHREC 2020: Multi-domain protein shape retrieval challenge.
Comput. Graph., 2020

SHREC 2020: Classification in cryo-electron tomograms.
Comput. Graph., 2020

Protein docking model evaluation by 3D deep convolutional neural networks.
Bioinform., 2020

A Simple But Effective Bert Model for Dialog State Tracking on Resource-Limited Systems.
Proceedings of the 2020 IEEE International Conference on Acoustics, 2020

2019
Study of the Variability of the Native Protein Structure.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

Three-dimensional Krawtchouk descriptors for protein local surface shape comparison.
Pattern Recognit., 2019

A global map of the protein shape universe.
PLoS Comput. Biol., 2019

Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0.
J. Comput. Aided Mol. Des., 2019

EnAET: Self-Trained Ensemble AutoEncoding Transformations for Semi-Supervised Learning.
CoRR, 2019

Prediction of protein group function by iterative classification on functional relevance network.
Bioinform., 2019

Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.
Bioinform., 2019

A Gated Self-attention Memory Network for Answer Selection.
Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing, 2019

Matching of EM Map Segments to Structurally-Relevant Bio-molecular Regions.
Proceedings of the High Performance Computing - 6th Latin American Conference, 2019



2018
IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Modeling the assembly order of multimeric heteroprotein complexes.
PLoS Comput. Biol., 2018

2017
Modeling disordered protein interactions from biophysical principles.
PLoS Comput. Biol., 2017

A Study of the Boltzmann Sequence-Structure Channel.
Proc. IEEE, 2017

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
BMC Bioinform., 2017

DextMP: deep dive into text for predicting moonlighting proteins.
Bioinform., 2017

Protein Shape Retrieval.
Proceedings of the 10th Eurographics Workshop on 3D Object Retrieval, 2017

2016
Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014.
J. Chem. Inf. Model., 2016

PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.
J. Chem. Inf. Model., 2016

Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations.
J. Comput. Chem., 2016

Genome-scale prediction of moonlighting proteins using diverse protein association information.
Bioinform., 2016

Ensemble-based evaluation for protein structure models.
Bioinform., 2016

The Boltzmann sequence-structure channel.
Proceedings of the IEEE International Symposium on Information Theory, 2016

2015
GenoBase: comprehensive resource database of <i>Escherichia coli</i> K-12.
Nucleic Acids Res., 2015

Navigating 3D electron microscopy maps with EM-SURFER.
BMC Bioinform., 2015

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.
Bioinform., 2015

PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool.
Bioinform., 2015

Phase transitions in a sequence-structure channel.
Proceedings of the 2015 Information Theory and Applications Workshop, 2015

2014
Comparison of Image Patches Using Local Moment Invariants.
IEEE Trans. Image Process., 2014

The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio.
Bioinform., 2014

2013
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.
BMC Bioinform., 2013

Evaluation of Arterial Stiffness during the Flow-Mediated Dilation Test.
Proceedings of the IEEE International Conference on Systems, 2013

2012
Effective inter-residue contact definitions for accurate protein fold recognition.
BMC Bioinform., 2012

Constructing patch-based ligand-binding pocket database for predicting function of proteins.
BMC Bioinform., 2012

Protein docking prediction using predicted protein-protein interface.
BMC Bioinform., 2012

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits.
BMC Bioinform., 2012

Protein domain recurrence and order can enhance prediction of protein functions.
Bioinform., 2012

2011
Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association.
BMC Bioinform., 2011

2010
Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map.
Int. J. Knowl. Discov. Bioinform., 2010

Improved protein surface comparison and application to low-resolution protein structure data.
BMC Bioinform., 2010

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP.
BMC Bioinform., 2010

2009
Application of 3D Zernike descriptors to shape-based ligand similarity searching.
J. Cheminformatics, 2009

Protein-protein docking using region-based 3D Zernike descriptors.
BMC Bioinform., 2009

3D-SURFER: software for high-throughput protein surface comparison and analysis.
Bioinform., 2009

ESG: extended similarity group method for automated protein function prediction.
Bioinform., 2009

2008
Combining gene sequence similarity and textual information for gene function annotation in the literature.
Inf. Retr., 2008

2007
Function Prediction of uncharacterized proteins.
J. Bioinform. Comput. Biol., 2007

Salient critical points for meshes.
Proceedings of the 2007 ACM Symposium on Solid and Physical Modeling, 2007

Tracing Lineage in Multi-version Scientific Databases.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences.
BMC Bioinform., 2006


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