Wherever data and models are available, I incorporate them directly into the construction of the animation, including molecular structures, dynamics simulations, speed measurements, and so on.
(a) Complex structures of the WW domain and proline rich motif (PRM); (b) Molecular structure of Gd@C82(OH)22; (c) Initial simulation system for the intrinsic binding dynamics of Gd@C82(on)22 on the WW domain; and (d) Initial system for the inhibitory dynamics of Gd@C82(OH)22 in competition with PRM.
The initial molecular structures for MD simulations were based on the X-ray crystallographic coordinates of NS by Ricagno et al. [15] for the native (PDB ID: 3F5N) and cleaved NSs (PDB ID: 3F02), and on analogy with the AAT structures [49,50] (for details see Appendix A, Supporting Table A1).
To confirm the stability of the molecular structures, we carry out simulations in explicit solvent using the CHARMM force field with explicit solvent [24].
In order to demonstrate the efficiency of this model, the relationships between hole mobilities and molecular structures were examined for 12 organic molecules to understand physical properties related to their mobilities in prepared amorphous structures by molecular dynamics simulations.
Asano, Y. & Kawahara, N. A New S -Hydroxynitrile Lyase from Baliospermum montanum —Its structure, molecular dynamics simulation, and improvement by protein engineering.
A crystal structure, molecular dynamics simulation and atomic mutagenesis studies suggest that nucleotides of an asymmetric bulge participate in the dynamic architecture of the ribozyme's active center.
Wei et al. [82] reported that the mechanical properties can be calculated for three types of CNF which have single or multishell nanocone or cone-stacked structure using molecular dynamics simulation and revealed the properties depended on the structure.
In the department, materials research includes studies in plasma etching, thin-film chemical vapor deposition, crystal growth, nano-crystalline structure, molecular simulation, scaffolds for bone and soft tissue regeneration, biocompatible polymers, and many other areas of materials engineering.
To understand the impact of single amino acid (missense) mutations on PFN1 structure, molecular dynamics simulations were performed in explicit solvent for PFN1WT, PFN1T109M, and PFN1G118V.
