Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations. - Shun Sakuraba; Akio Kitao (J. Comput. Chem., 2009)

Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules. - Jinzen Ikebe; Shun Sakuraba; Hidetoshi Kono (J. Comput. Chem., 2014)

Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions. - Shun Sakuraba; Nobuyuki Matubayasi (J. Comput. Chem., 2014)

Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs). - Hongchun Li; Shun Sakuraba; Aravind Chandrasekaran; Lee-Wei Yang (J. Chem. Inf. Model., 2014)

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation. - Jinzen Ikebe; Shun Sakuraba; Hidetoshi Kono (PLoS Comput. Biol., 2016)

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. - Taichi Hagio; Shun Sakuraba; Junichi Iwakiri; Ryota Mori; Kiyoshi Asai (BMC Bioinform., 2018)

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software. - Shun Sakuraba; Ikuo Fukuda (J. Comput. Chem., 2018)

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. - Hidetoshi Kono; Shun Sakuraba; Hisashi Ishida (PLoS Comput. Biol., 2018)

Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. - Hidetoshi Kono; Shun Sakuraba; Hisashi Ishida (PLoS Comput. Biol., 2019)

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. - Shimpei Nishida; Shun Sakuraba; Kiyoshi Asai; Michiaki Hamada (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Large-Scale Parallel Implementation of Hartree-Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform. - Hideaki Takahashi; Shun Sakuraba; Akihiro Morita (J. Chem. Inf. Model., 2020)

Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex. - Shun Sakuraba; Qilin Xie; Kota Kasahara; Junichi Iwakiri; Hidetoshi Kono (PLoS Comput. Biol., 2022)

Mechanistic Insights into HP1α CSD Oligomerization and the Role of PxVxL Motif-Containing Proteins. - Amarjeet Kumar; Shun Sakuraba; Nitika Gaurav; Karthik Selvam; Tatiana G. Kutateladze; Hidetoshi Kono (J. Chem. Inf. Model., 2025)