Publications

International Journal (Peer-reviewed)

  1. Furui K, and Ohue M. "ALLM-Ab: Active Learning-driven antibody optimization using fine-tuned protein Language Models." J. Chem. Inf. Model. 65.21, 11543-11557, 2025. doi: 10.1021/acs.jcim.5c01577
  2. Furui K, Sakano K, Ohue M. "Predictive and therapeutic applications of protein language models." Allergol. Int. 74.4, 534-548, 2025. doi: 10.1016/j.alit.2025.08.004
  3. Uchikawa K, Furui K, and Ohue M. "Leveraging AlphaFold2 Structural Space Exploration for Generating Drug Target Structures in Structure-Based Virtual Screening" Biochem. Biophy. Rep. 43, 102110, 2025. doi: 10.1016/j.bbrep.2025.102110
  4. Furui K, and Ohue M. "Benchmarking HelixFold3-Predicted Holo Structures for Relative Free Energy Perturbation Calculations" ACS Omega. 10.11, 11411-11420, 2025. doi: 10.1021/acsomega.4c11413
  5. Furui K, Shimizu T, Akiyama Y, Kimura S R, Terada Y, and Ohue M. "PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations" J. Chem. Inf. Model. 65.2, 705–721, 2025. doi: 10.1021/acs.jcim.4c01634
  6. Sakano K, Furui K, Ohue M. "NPGPT: natural product-like compound generation with GPT-based chemical language models" J. Supercomput. 81.1, 1-16, 2025. doi: 10.1007/s11227-024-06860-w
  7. Furui K, Ohue M. "Fastlomap: faster lead optimization mapper algorithm for large-scale relative free energy perturbation" J. Supercomput. 2024. doi: 10.1007/s11227-024-06006-y
  8. Ochiai T, Inukai T, Akiyama M, Furui K, Ohue M, Matsumori N, Inuki S, Uesugi M, Sunazuka T, Kikuchi K, Kakeya H & Sakakibara Y. "Variational autoencoder-based chemical latent space for large molecular structures with 3D complexity." Commun. Chem. 6, 249, 2023. doi: 10.1038/s42004-023-01054-6

International Conference (Peer-reviewed)

  1. Furui K, and Ohue M. "Boltzina: Efficient and Accurate Virtual Screening via Docking-Guided Binding Prediction with Boltz-2." AI for Accelerated Materials Design Workshop at the 39th Conference on Neural Information Processing Systems (AI4Mat workshop on NeurIPS2025), 2025. [link]
  2. Masunaga S†, Furui K†, Kengkanna A, Ohue M. "GraphBioisostere: General Bioisostere Prediction Model with Deep Graph Neural Network." In Proc PDPTA'25, IEEE CPS, 2025. (†: equally contributed)
  3. Ohue M, Furui K. "GBDT-based Model and Web Tool for Prediction of Blood-Placental Barrier Permeability of Small Molecules." In Proc PDPTA'25, IEEE CPS, 2025.
  4. Furui K, and Ohue M. "Active learning for energy-based antibody optimization and enhanced screening." Machine Learning in Structural Biology Workshop at the 38th Conference on Neural Information Processing Systems (MLSB workshop on NeurIPS2024), 2024. [link]
  5. Sakano K, Furui K, Ohue M. "Natural Product-like Compound Generation with Chemical Language Models." In Proc PDPTA'24, IEEE CPS, 2024.
  6. Murakumo K, Yoshikawa N, Kentaro R, Nakamura S, Furui K, Suzuki T Yamasaki H, Nishigaya Y, Takagi Y & Ohue M. "LLM Drug Discovery Challenge: A Contest as a Feasibility Study on the Utilization of Large Language Models in Medicinal Chemistry." AI for Accelerated Materials Design-NeurIPS 2023 Workshop, 2023. [link]
  7. Furui K, and Ohue M. "Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation." In Proc PDPTA'23, IEEE CPS, 2023.
  8. Furui K, and Ohue M "Compound Virtual Screening by Learning-to-Rank with Gradient Boosting Decision Tree and Enrichment-based Cumulative Gain." 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2022. doi: 10.1109/CIBCB55180.2022.9863032

Preprints

  1. Arai M, Makita Y, Saito S, Suzuki S, Narushima Y, Izawa N, Tanaka Y, Furui K, Ohue M, Ishibashi M. "The Indole Rocaglamide Induces S and G2/M Phase Cell Cycle Arrest in Small Cell Lung Cancer Cells Through ASCL1 Translation Inhibition." Available at SSRN preprint 4493242. doi: 10.2139/ssrn.4493242

International Conference (Non-Peer-reviewed)

  1. Furui K, Ohue M. "Active Learning-Driven Antibody Optimization Using Fine-tuned Protein Language Models" ORG004: Bio-Active Molecular Design Interwoven By AI Technology, Chemical Biology And Organic Synthesis, PacifiChem2025, 2025. (Oral)
  2. Masunaga S, Furui K, Kengkanna A, Ohue M. "Predicting Bioactivity Differences of Molecular Pairs Using Graph Neural Networks" ORG004: Bio-Active Molecular Design Interwoven By AI Technology, Chemical Biology And Organic Synthesis, PacifiChem2025, 2025. (Poster)
  3. Sakano K, Furui K, Ohue M. "Stereochemistry-Aware Molecular Generation Method Based on Chemical Language Models" ORG004: Bio-Active Molecular Design Interwoven By AI Technology, Chemical Biology And Organic Synthesis, PacifiChem2025, 2025. (Poster)
  4. Furui K, Ohue M. "ALLM-Ab: Active Learning-Driven Antibody Optimization Using Fine-tuned Protein Language Models." Asia Hub for e-Drug Discovery 2025 (AHeDD2025), 2025. (Poster)