Publications
Novel binding site on clathrin and adaptors regulate distinct aspects of coat assembly. Traffic (2006) 7(12): 1688-1700Mutagenesis and Ota's modeling studies revealed a novel clathrin box
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J. Mol. Biol. (2005) 351: 345-354
Ota's anisotropic thermal diffusion (ATD) modeling revealed an intramolecular signaling pathway in a PDZ domain protein family, and this was later confirmed by site directed mutagenesis studies
Clathrin light and heavy chain interface: a-helix binding superhelix loops via critical tryptophans. EMBO J (2002) 21922):6072-6082
Genetic and modeling structural studies of light chain binding were mapped and subjected to mutations to confirm the binding role
Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement. J. Mol. Biol. (2001) 314:607-617
Ota method predicted VSV8 peptide binding to MHC and confirmed experimentally
The 0.83 A resolution crystal structure of a-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain. J. Mol. Biol. (2004); 338(5):999-1013
First high resolution analysis of a serine protease active site and modeling of alternative conformations
Non-Boltzman thermodynamic integration (NBTI) for macromolecular systems; relative free energy of binding of trypsin to benzamidine and benzylamine. PROTEINS: Structure, Function, and Genetics (1999); 37: 641-653
Ota algorithm calculation of relative free energies and compared to crystal structures, showing that the algorithm gave data close to experimental data
Overcoming barriers in macromolecular simulations: non-Boltzmann thermodynamic integration. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) (1998); 98(4):171-181
Ota method for more accurate free energy calculation