Journal of Chemical Information and Modeling 60(11) 5382-5394 2020年11月 [査読有り]
The accurate prediction of protein-ligand binding affinity is a central challenge in computational chemistry and in-silico drug discovery. The free energy perturbation (FEP) method based on molecular dynamics (MD) simulation provides reasonably ac...
Seonghoon Kim Hiraku Oshima Han Zhang Nathan R. Kern Suyong Re Jumin Lee Benoît Roux Yuji Sugita Wei Jiang Wonpil Im
Journal of Chemical Theory and Computation 16(11) 7207-7218 2020年11月 [査読有り]
Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling m...
The journal of physical chemistry letters 11(5) 1934-1939 2020年3月 [査読有り]
Slow polypeptide conformational changes on time scales of >1 s are generally assumed to be highly cooperative two-state transitions, reflecting the high energy barrier. However, few experimental characterizations have tested the validity of this a...
Ai Niitsu Suyong Re Hiraku Oshima Motoshi Kamiya Yuji Sugita
Journal of chemical information and modeling 59(9) 3879-3888 2019年9月 [査読有り]
Molecular recognition underpins all specific protein-ligand interactions and is essential for biomolecular functions. The prediction of canonical binding poses and distinguishing binders from nonbinders are much sought after goals. Here, we apply ...
大学本部
理学研究科