Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. - Shandar Ahmad; Yumlembam Hemjit Singh; Yogesh Paudel; Takaharu Mori; Yuji Sugita; Kenji Mizuguchi (BMC Bioinform., 2010)

Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods. - Takaharu Mori; Fumiko Ogushi; Yuji Sugita (J. Comput. Chem., 2012)

Efficient lookup table using a linear function of inverse distance squared. - Jaewoon Jung; Takaharu Mori; Yuji Sugita (J. Comput. Chem., 2013)

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. - Jaewoon Jung; Takaharu Mori; Yuji Sugita (J. Comput. Chem., 2014)

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. - Chigusa Kobayashi; Jaewoon Jung; Yasuhiro Matsunaga; Takaharu Mori; Tadashi Ando; Koichi Tamura; Motoshi Kamiya; Yuji Sugita (J. Comput. Chem., 2017)

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. - Osamu Miyashita; Chigusa Kobayashi; Takaharu Mori; Yuji Sugita; Florence Tama (J. Comput. Chem., 2017)

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. - Takaharu Mori; Genki Terashi; Daisuke Matsuoka; Daisuke Kihara; Yuji Sugita (J. Chem. Inf. Model., 2021)

SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. - Isseki Yu; Takaharu Mori; Daisuke Matsuoka; Donatas Surblys; Yuji Sugita (J. Comput. Chem., 2024)