Shun Sakuraba

Publication Activity (10 Years)

Years Active: 2009-2022
Publications (10 Years): 8

Top Topics

Influenza Virus

Secondary Structure

Generalized Belief Propagation

Top Venues

PLoS Comput. Biol.

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono
Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex. PLoS Comput. Biol. 18 (1) (2022)
Hideaki Takahashi, Shun Sakuraba, Akihiro Morita
Large-Scale Parallel Implementation of Hartree-Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform. J. Chem. Inf. Model. 60 (3) (2020)
Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida
Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. PLoS Comput. Biol. 15 (10) (2019)
Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. PLoS Comput. Biol. 14 (3) (2018)
Shun Sakuraba, Ikuo Fukuda
Performance evaluation of the zero-multipole summation method in modern molecular dynamics software. J. Comput. Chem. 39 (20) (2018)
Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. BMC Bioinform. (1) (2018)
Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono
H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation. PLoS Comput. Biol. 12 (3) (2016)
Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono
Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules. J. Comput. Chem. 35 (1) (2014)
Hongchun Li, Shun Sakuraba, Aravind Chandrasekaran, Lee-Wei Yang
Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs). J. Chem. Inf. Model. 54 (8) (2014)
Shun Sakuraba, Nobuyuki Matubayasi
Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions. J. Comput. Chem. 35 (21) (2014)
Shun Sakuraba, Akio Kitao
Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations. J. Comput. Chem. 30 (12) (2009)