DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. - Wataru Nishima; Guoying Qi; Steven Hayward; Akio Kitao (Bioinform., 2009)

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. - Lee-Wei Yang; Eran Eyal; Ivet Bahar; Akio Kitao (Bioinform., 2009)

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

Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. - Nick Matthews; Akio Kitao; Stephen D. Laycock; Steven Hayward (J. Chem. Inf. Model., 2019)

Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM. - Mohamed Marzouk Sobeh; Akio Kitao (J. Chem. Inf. Model., 2022)

RNA Binding Mechanism of the FUS Zinc Finger in Concert with Its Flanking Intrinsically Disordered Region. - Soichiro Kijima; Akio Kitao (J. Chem. Inf. Model., 2025)

Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study. - Georgios Iakovou; L. Palmer; A. Ganesan; Akio Kitao; Stephen D. Laycock; Steven Hayward (J. Comput. Aided Mol. Des., 2025)