2004- PhD, School of Science, Kyoto University
2004- Postdoctoral Researcher, School of Arts and Sciences, The University of Tokyo (UTokyo)
2007- Postdoctoral Researcher, Department of Chemistry, University of Utah
2010- Postdoctoral Researcher, Department of Chemistry, University of Chicago
2011- Project Associate Professor, RCAST, UTokyo
FIELD OF INTEREST
At the molecular level, biological phenomena can be regarded as a complicated but well-designed network of reactions including not only chemical bond alternation, but also the structural change or docking of proteins. Deterioration, of even just a single element of the network may lead to a wide variety of diseases, including cancer. Therefore, it is important to understand and predict the molecular mechanisms that lead to or prevent the deterioration of the network. We study the behavior of biological molecules related to serious diseases at the molecular level by using theoretical calculations, mainly in molecular dynamics simulations. We aim to extract information essential for drug design from those calculations. Also we are developing a new method for estimating critical properties based on basic physics and theoretical chemistry.
- Molecular dynamics analysis to evaluate docking pose prediction. Sakano T, Mahamood MI, Yamashita T, Fujitani H.Biophys Physicobiol. 2016;13:181-194. doi: 10.2142/biophysico.13.0_181 The feasibility of an efficient drug design method with high-performance computers. Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T, Fujitani H.Chem. Pharm. Bull. 2015;63(3):147-55. doi: 10.1248/cpb.c14-00596 Molecular dynamics simulation-based evaluation of the binding free energies of computationally designed drug candidates: importance of the dynamical effects. Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T, Fujitani H.Chem. Pharm. Bull. 2014;62(7):661-7. doi: 10.1248/cpb.c14-00132 Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses. Nakayama T, Mizohata E, Yamashita T, Nagatoishi S, Nakakido M, Iwanari H, Mochizuki Y, Kado Y, Yokota Y, Satoh R, Tsumoto K, Fujitani H, Kodama T, Hamakubo T, Inoue T.Protein Sci. 2015 Mar;24(3):328-40. doi: 10.1002/pro.2619 On accurate calculation of the potential of mean force between antigen and antibody: A case of the HyHEL-10-hen egg white lysozyme system T. Yamashita and H. FujitaniChem Phys Lett. 2014, v. 609, pp. 50-53 https://doi.org/10.1016/j.cplett.2014.06.028 On the origin of proton mobility suppression in aqueous solutions of amphiphiles. Xu J, Yamashita T, Agmon N, Voth GA.J Phys Chem B. 2013 Dec 12;117(49):15426-35. doi: 10.1021/jp4051726 High Performance Computing for Drug Development on K computer H. Fujitani, K. Shinoda, T. Yamashita, T. KodamaJ Phys: Conf Ser. 2013, 454, p. 012018. doi: 10.1088/1742-6596/454/1/012018 Energy quantization of chaos with the semiclassical phases alone. Takatsuka K, Takahashi S, Koh YW, Yamashita T.J Chem Phys. 2007 Jan 14;126(2):021104. doi: 10.1063/1.2431178 Excited state electronic structures and dynamics of NOCl: a new potential function set, absorption spectrum, and photodissociation mechanism. Yamashita T, Kato S.J Chem Phys. 2004 Aug 01;121(5):2105-16. doi: 10.1063/1.1768158