ProTherm: Thermodynamic Database for Proteins and Mutants. - M. Michael Gromiha; Jianghong An; Hidetoshi Kono; Motohisa Oobatake; Hatsuho Uedaira; Akinori Sarai (Nucleic Acids Res., 1999)

Multicanonical Monte Carlo calculation of the free-energy map of the base-amino acid interaction. - Kenji Sayano; Hidetoshi Kono; M. Michael Gromiha; Akinori Sarai (J. Comput. Chem., 2000)

ProTherm, version 2.0: thermodynamic database for proteins and mutants. - M. Michael Gromiha; Jianghong An; Hidetoshi Kono; Motohisa Oobatake; Hatsuho Uedaira; Ponraj Prabakaran; Akinori Sarai (Nucleic Acids Res., 2000)

Thermodynamic database for protein-nucleic acid interactions (ProNIT). - Ponraj Prabakaran; Jianghong An; M. Michael Gromiha; Samuel Selvaraj; Hatsuho Uedaira; Hidetoshi Kono; Akinori Sarai (Bioinform., 2001)

Structure-Function Relationship in DNA Sequence Recognition by Transcription Factors. - Akinori Sarai; Samuel Selvaraj; M. Michael Gromiha; Hidetoshi Kono (APBC, 2004)

Progress in the development and application of computational methods for probabilistic protein design. - Sheldon Park; Hidetoshi Kono; Wei Wang; Eric T. Boder; Jeffery G. Saven (Comput. Chem. Eng., 2005)

Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism. - Akinori Sarai; Jorg Siebers; Samuel Selvaraj; M. Michael Gromiha; Hidetoshi Kono (J. Bioinform. Comput. Biol., 2005)

Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach. - Marcos J. Araúzo-Bravo; Satoshi Fujii; Hidetoshi Kono; Akinori Sarai (APBC, 2006)

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. - Shandar Ahmad; Hidetoshi Kono; Marcos J. Araúzo-Bravo; Akinori Sarai (Nucleic Acids Res., 2006)

coliSNP database server mapping nsSNPs on protein structures. - Hidetoshi Kono; Tomo Yuasa; Shinya Nishiue; Kei Yura (Nucleic Acids Res., 2008)

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

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)

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)