Multiplicity in Long Noncoding RNA Biomedical Sciences

R. Kurokawa, R. Komiya, T. Oyoshi, Y. Matsuno, H. Tani, M. Katahira, K. Hitachi, Y. Iwashita, T. Yamashita, K. Kondo, R. Yoneda, Y. Yamaoki, N. Ueda, T. Mashima, N. Kobayashi, T. Nagata, A. Kiyoishi, M. Miyake, F. Kano, M. Murata1, N. Hamad, K. Sasaki, N. Shoji Multiplicity in Long Noncoding RNA Biomedical Sciences Biomedical Sciences 4, 18-23 (2018)

Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody

K. Miyanabe, T. Yamashita, Y. Abe, H. Akiba, Y. Takamatsu, M. Nakakido, T. Hamakubo, T. Ueda, J. Caaveiro, K. Tsumoto,

Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody Biochemistry, 57 (28), pp 4177–4185 (2018) DOI: 10.1021/acs.biochem.8b00592

Toward rational antibody design: recent advancements in molecular dynamics simulations

T. Yamashita Toward rational antibody design: recent advancements in molecular dynamics simulations Int. Immunol., 30, 133–140 (2018) doi: 10.1093/intimm/dxx077

An Ensemble Docking Calculation of Lysozyme and HyHEL-10: Insight into the Binding Mechanism

T. Yamashita and Y. Takamatsu An Ensemble Docking Calculation of Lysozyme and HyHEL-10: Insight into the Binding Mechanism AIP Conf. Proc. 2017, 1906, 030022 https://doi.org/10.1063/1.5012301

京速コンピューティングによる創薬への挑戦: ポスト「京」時代に向けて

山下雄史 京速コンピューティングによる創薬への挑戦: ポスト「京」時代に向けて 分子シミュレーション研究会会誌「アンサンブル」19(2) 81-87 (2017) https://doi.org/10.11436/mssj.19.81

Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories

Yamashita T. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories Biomedical Sciences 2016, V. 2 (5), pp. 34-47 doi: 10.11648/j.bs.20160205.11

On the accurate molecular dynamics analysis of biological molecules

Yamashita T. On the accurate molecular dynamics analysis of biological molecules AIP Conf Proc. 2016, 1790, 020026; doi: http://dx.doi.org/10.1063/1.4968652

Molecular dynamics analysis to evaluate docking pose prediction.

Sakano T, Mahamood MI, Yamashita T, Fujitani H. Molecular dynamics analysis to evaluate docking pose prediction. Biophys Physicobiol. 2016 Jul 14;13:181-194. eCollection 2016.

Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations

Yamashita T. Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations JPS Conf Proc. 2015, v. 5, p. 010003, DOI: http://dx.doi.org/10.7566/JPSCP.5.010003

自由エネルギー計算の理論: 創薬応用を実現する定量的予測への挑戦

山下雄史 自由エネルギー計算の理論: 創薬応用を実現する定量的予測への挑戦 分子シミュレーション研究会会誌“アンサンブル” Vol. 17 (2), 83-91 (2015) 2015年4月 http://doi.org/10.11436/mssj.17.83

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. The feasibility of an efficient drug design method with high-performance computers. Chem Pharm Bull (Tokyo). 2015;63(3):147-55. doi: 10.1248/cpb.c14-00596.

Properties of a Hydrated Excess Proton Near the Cholesterol-Containing Phospholipid Bilayer

Yamashita T. Properties of a Hydrated Excess Proton Near the Cholesterol-Containing Phospholipid Bilayer JPS Conf Proc. 2014, v. 1, p. 013086; DOI: http://dx.doi.org/10.7566/JPSCP.1.013086

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. Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses. Protein Sci. 2015 Mar;24(3):328-40. doi: 10.1002/pro.2619. Epub 2015 Jan 13.

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. Molecular dynamics simulation-based evaluation of the binding free energies of computationally designed drug candidates: importance of the dynamical effects. Chem Pharm Bull (Tokyo). 2014;62(7):661-7.

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. Fujitani On accurate calculation of the potential of mean force between antigen and antibody: A case of the HyHEL-10-hen egg white lysozyme system Chem 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. On the origin of proton mobility suppression in aqueous solutions of amphiphiles. J Phys Chem B. 2013 Dec 12;117(49):15426-35. doi: 10.1021/jp4051726. Epub 2013 Jul 22.