Automatic Improvement of Scheduling Policies in Parsley Parallel Programming Environment. - Masakazu Sekijima; Shinya Takasaki; Shugo Nakamura; Kentaro Shimizu (IASTED PDCS, 2002)

Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing. - Masakazu Sekijima; Chie Motono; Satoshi Yamasaki; Kiyotoshi Kaneko; Yutaka Akiyama (ISHPC, 2003)

High-Density Surface Reconstruction of Fine Arts and Documents for Complete Reproduction and Counterfeit Detection. - Junta Doi; Kentaro Shimizu; Masakazu Sekijima (ICNSC, 2007)

Optimization and evaluation of parallel molecular dynamics simulation on blue gene/L. - Masakazu Sekijima; Junta Doi; Tamotsu Noguchi; Yutaka Akiyama; Shigenori Shimizu (Parallel and Distributed Computing and Networks, 2007)

Development of Molecular Dynamics Simulation Based Flexible Docking System. - Sachi Kimura; Masakazu Sekijima; Masami Takata; Tamotsu Noguchi; Kazuki Joe (PDPTA, 2007)

Development of an SVM based Prediction System for Metalbinding Sites in Protein. - Masami Nakazawa; Masami Takata; Kiyonobu Yokota; Tamotsu Noguchi; Masakazu Sekijima; Kazuki Joe (PDPTA, 2007)

Optimization of Molecular Dynamics Simulation on Cell Processor. - Manami Sasaki; Masakazu Sekijima; Masami Takata; Kazuki Joe (PDPTA, 2007)

Large-Scale Computing for Protein-Protein Binding Free Energy Calculation. - Junichi Ikeda; Kazuki Ohno; Sayaka Akioka; Masaya Orita; Yoichi Muraoka; Tamotsu Noguchi; Masakazu Sekijima (PDPTA, 2008)

Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation. - Masakazu Sekijima; Junta Doi; Shinya Honda; Tamotsu Noguchi; Shigenori Shimizu; Yutaka Akiyama (Inf. Media Technol., 2008)

The Power Efficiency of GPUs in Multi Nodes Environment with Molecular Dynamics. - Takuro Udagawa; Masakazu Sekijima (ICPP Workshops, 2011)

Distance-based Factor Graph Linearization and Sampled Max-sum Algorithm for Efficient 3D Potential Decoding of Macromolecules. - Takahiro Shinozaki; Toshinao Iwaki; Shiqiao Du; Masakazu Sekijima; Sadaoki Furui (Inf. Media Technol., 2012)

GPU Accelerated Molecular Dynamics with Method of Heterogeneous Load Balancing. - Takuro Udagawa; Masakazu Sekijima (IPDPS Workshops, 2015)

Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. - Katie Wilkins; Mehedi Hassan; Margherita Francescatto; Jakob B. Jespersen; R. Gonzalo Parra; Bart Cuypers; Dan F. DeBlasio; Alexander Junge; Anupama Jigisha; Farzana Rahman; Griet Laenen; Sander Willems; et al. (BMC Bioinform., 2016)

CoDe-DTI: Collaborative Deep Learning-based Drug-Target Interaction Prediction. - Nobuaki Yasuo; Yusuke Nakashima; Masakazu Sekijima (BIBM, 2018)

Compound property enhancement by virtual compound synthesis. - Naoki Arai; Shunsuke Yoshikawa; Nobuaki Yasuo; Ryunosuke Yoshino; Masakazu Sekijima (J. Bioinform. Comput. Biol., 2018)

Web Molecular Graphics: Emerging Technologies & Standards (NII Shonan Meeting 2018-19). - Seán I. O'Donoghue; Masakazu Sekijima; Marc Baaden (NII Shonan Meet. Rep., 2018)

Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning. - Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2019)

ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. - Sherlyn Jemimah; Masakazu Sekijima; M. Michael Gromiha (Bioinform., 2020)

MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning. - Daiki Erikawa; Nobuaki Yasuo; Masakazu Sekijima (J. Cheminformatics, 2021)

An Improved Model for Predicting Compound Retrosynthesizability Using Machine Learning. - Mami Ozawa; Nobuaki Yasuo; Masakazu Sekijima (BIBE, 2022)

Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides. - Kazuki Z. Yamamoto; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2022)

IEV2Mol: Molecular Generative Model Considering Protein-Ligand Interaction Energy Vectors. - Mami Ozawa; Shogo Nakamura; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2024)

Mothra: Multiobjective de novo Molecular Generation Using Monte Carlo Tree Search. - Takamasa Suzuki; Dian Ma; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2024)

PRA-MutPred: Predicting the Effect of Point Mutations in Protein-RNA Complexes Using Structural Features. - K. Harini; Masakazu Sekijima; M. Michael Gromiha (J. Chem. Inf. Model., 2025)

DiffInt: A Diffusion Model for Structure-Based Drug Design with Explicit Hydrogen Bond Interaction Guidance. - Masami Sako; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2025)