Author details

Full Name

Masahito Ohue

Affiliation

ORCID

Career Start Year

2011

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37363399	Editorial: Web tools for modeling and analysis of biomolecular interactions Volume II.	Front Mol Biosci	2023
37737185	MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory.		2023
37570623	Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties.		2023
37973971	Variational autoencoder-based chemical latent space for large molecular structures with 3D complexity.		2023
37686057	Design of Cyclic Peptides Targeting Protein-Protein Interactions Using AlphaFold.		2023
36930969	CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides.		2023
34849593	Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning.		2022
35884931	Solubility-Aware Protein Binding Peptide Design Using AlphaFold.	Biomedicines	2022
35480880	Editorial: Web Tools for Modeling and Analysis of Biomolecular Interactions.	Front Mol Biosci	2022
36061673	Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation.	ACS Omega	2022
36053061	Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations.	Journal of Chemical Information and Modeling	2022
34573438	Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets.	Genes	2021
34236179	Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations.	Journal of Chemical Information and Modeling	2021
34069916	Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis.	International Journal of Molecular Sciences	2021
34681589	Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions.	International Journal of Molecular Sciences	2021
32509489	Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces.	Biophysics and physicobiology	2020
33195406	Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein-Protein Docking Poses.	Front Mol Biosci	2020
33183011	Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.	Journal of Medicinal Chemistry	2020
31377536	Learning-to-rank technique based on ignoring meaningless ranking orders between compounds.	Journal of Molecular Graphics and Modelling	2019
31863054	A prospective compound screening contest identified broader inhibitors for Sirtuin 1.	Sci Rep	2019
30596417	Synthesis of Triazolo- and Oxadiazolopiperazines by Gold(I)-Catalyzed Domino Cyclization: Application to the Design of a Mitogen Activated Protein (MAP) Kinase Inhibitor.	Organic Letters	2019
29971617	QEX: target-specific druglikeness filter enhances ligand-based virtual screening.	Molecular Diversity	2019
30793050	NRLMF: Beta-distribution-rescored neighborhood regularized logistic matrix factorization for improving the performance of drug-target interaction prediction.	Biochemistry and Biophysics Reports	2019
29197725	Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach.	Journal of Molecular Graphics and Modelling	2018
30598072	Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques.	BMC Bioinformatics	2018
30273347	The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency.	PLoS ONE	2018
29628156	Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm.		2018
29482137	Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem.		2018
29745830	MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.	BMC Bioinformatics	2018
27830312	Rigid-Docking Approaches to Explore Protein-Protein Interaction Space.	Advances in Biochemical Engineering/Biotechnology	2017
28451968	GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data.	Methods in Molecular Biology	2017
28369284	Spresso: an ultrafast compound pre-screening method based on compound decomposition.		2017
27924264	Specificity of broad protein interaction surfaces for proteins with multiple binding partners.	Biophysics and physicobiology	2016
25707855	Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures.	BMC Systems Biology	2015
25100686	MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.		2014
23855673	MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.	Protein and Peptide Letters	2014
23855669	Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis.	Protein and Peptide Letters	2014
24564962	Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods.	BMC Proceedings	2013
23874954	Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.	PLoS ONE	2013
24004986	MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.	Source Code for Biology and Medicine	2013
22001016	Community-wide assessment of protein-interface modeling suggests improvements to design methodology.	J Mol Biol	2011
22230937	Docking-calculation-based method for predicting protein-RNA interactions.	Genome informatics. International Conference on Genome Informatics	2011