Masahito Ohue - RankMe

49 papers B 2C 5Journal 33Unranked 9

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	GraphBioisostere: general bioisostere prediction model with deep graph neural network. J. Supercomput. Sho Masunaga, Kairi Furui, Apakorn Kengkanna, Masahito Ohue
2026	J	`jnl`	PBPredictor.net: GBDT-based model and web tool for prediction of blood-placental barrier permeability of small molecules. J. Supercomput. Masahito Ohue, Kairi Furui
2025	J	`jnl`	ALLM-Ab: Active Learning-Driven Antibody Optimization Using Fine-Tuned Protein Language Models. J. Chem. Inf. Model. Kairi Furui, Masahito Ohue
2025	J	`jnl`	Boltzina: Efficient and Accurate Virtual Screening via Docking-Guided Binding Prediction with Boltz-2. CoRR Kairi Furui, Masahito Ohue
2025	J	`jnl`	Innovations in mathematical modeling, AI, and optimization techniques. J. Supercomput. Masahito Ohue, Nobuaki Yasuo, Masami Takata
2025	J	`jnl`	NPGPT: natural product-like compound generation with GPT-based chemical language models. J. Supercomput. Koh Sakano, Kairi Furui, Masahito Ohue
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`	Active learning for energy-based antibody optimization and enhanced screening. CoRR Kairi Furui, Masahito Ohue
2024	J	`jnl`	Antibody complementarity-determining region design using AlphaFold2 and DDG predictor. J. Supercomput. Takafumi Ueki, Masahito Ohue
2024	J	`jnl`	Fastlomap: faster lead optimization mapper algorithm for large-scale relative free energy perturbation. J. Supercomput. Kairi Furui, Masahito Ohue
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`	Mathematical modeling and problem solving: from fundamentals to applications. J. Supercomput. Masahito Ohue, Kotoyu Sasayama, Masami Takata
2024	J	`jnl`	NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models. CoRR Koh Sakano, Kairi Furui, Masahito Ohue
2024	—	`conf`	Predicting Antibody Stability pH Values from Amino Acid Sequences: Leveraging Protein Language Models for Formulation Optimization. BIBM Takuya Tsutaoka, Noriji Kato, Toru Nishino, Yuanzhong Li, Masahito Ohue
2024	—	`conf`	REALM: Region-Empowered Antibody Language Model for Antibody Property Prediction. BIBM Toru Nishino, Noriji Kato, Takuya Tsutaoka, Yuanzhong Li, Masahito Ohue
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
2023	J	`jnl`	Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction. CoRR Apakorn Kengkanna, Masahito Ohue
2023	C	`conf`	Enhancing Model Learning and Interpretation using Multiple Molecular Graph Representations for Compound Property and Activity Prediction. CIBCB Apakorn Kengkanna, Masahito Ohue
2023	J	`jnl`	Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation. CoRR Kairi Furui, Masahito Ohue
2022	C	`conf`	Compound Virtual Screening by Learning-to-Rank with Gradient Boosting Decision Tree and Enrichment-based Cumulative Gain. CIBCB Kairi Furui, Masahito Ohue
2022	J	`jnl`	Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain. CoRR Kairi Furui, Masahito Ohue
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
2021	C	`conf`	Drug-target affinity prediction using applicability domain based on data density. CIBCB Shunya Sugita, Masahito Ohue
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
2021	C	`conf`	Quantitative Estimate of Protein-Protein Interaction Targeting Drug-likeness. CIBCB Takatsugi Kosugi, Masahito Ohue
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`	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`	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
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`	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