Nobuyuki Ota

Publications:

Ota N, Agard DA. "Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion." J Mol Biol. 2005 Jul 7; (html or pdf)

Fuhrmann, C.N., Kelch, B.A., Ota, N., Agard, D.A. "The 0.83Å resolution crystal structure of alpha-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. (html or pdf)

Chih-Ying Chen, Michael L. Reese, Peter K. Hwang, Nobuyuki Ota, David Agard, and Frances M. Brodsky (2002). Clathrin light and heavy chain interface: a-helix binding superhelix loops via critical tryptophans, The EMBO Journal, 21(22), 6072-6082 (html or pdf).

Gwen Tatsuno, John Anderson, Jin Hong, David A. Agard, Nobuyuki Ota, Sukanto Sinha, Guriqbal Basi and Lisa McConlogue (2001) "Functional Analysis of b-Secretase Using Mutagenesis and Structural Homology Modeling." in Alzheimer's Disease: Advances in Etiology, Pathogenesis and Therapeutics. (K. Iqbal, S. S. Sisodia & B. Winblad, eds), John Weily & Sons, Ltd. (book)

"Binding Mode Prediction for a Flexible Ligand in a Flexible Pocket using Multi-Conformation Simulated Annealing Pseudo Crystallographic Refinement", Ota, Nobuyuki and Agard, David A., J. Mol. Biol. (2001), 314(3), 607-17 (pdf or html). 

"Enzyme specificity under dynamic control II: Principal component analysis of a-lytic protease using global and local solvent boundary conditions," Ota, Nobuyuki and Agard, David A., Protein Sci. (2001), 10(7), 1403-1414 (pdf or html).

"Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine," Ota N, Stroupe C, Ferreira-da-Silva JM, Shah SA, Mares-Guia M, Brunger AT., Proteins: Struct., Funct., Genet. 1999, 37(4), 641-53 (html).

"Overcoming barriers in macromolecular simulations. Non-Boltzmann thermodynamic integration," Ota, Nobuyuki; Bruenger, Axel T., Theor. Chem. Acc. (1997), 98(4), 171-181.