Zobrazeno 81 - 90
of 173
pro vyhledávání: '"Ray Luo"'
Publikováno v:
Journal of Chemical Theory and Computation. 6:1157-1169
A revised density function is developed to define the molecular surface for the numerical Poisson-Boltzmann methods to achieve a better convergence and higher numerical stability. The new density function does not use any predefined functional form b
Publikováno v:
Biophysical Journal. 114:432a
Autor:
Ray Luo, Meng-Juei Hsieh
Publikováno v:
The Journal of Physical Chemistry B. 114:2886-2893
We have analyzed the quality of a recently proposed Amber united-atom model and its overall efficiency in ab initio folding and thermodynamic sampling of two stable beta-hairpins. It is found that the mean backbone structures are quite consistent bet
Publikováno v:
Phys. Chem. Chem. Phys.. 12:1194-1202
A critical issue in the development of implicit solvent models is their quality in realistic simulations of non-trivial systems. In a previous study, we quantitatively compared the reaction field energies of static structures calculated with the Pois
Autor:
Yu-Hong Tan, Vira Tretyachenko-Ladokhina, Xiang Ye, Wei Yang, Y. Morris Chen, Qiang Lu, Donald F. Senear, Ray Luo
Publikováno v:
Biophysical Chemistry. 145:37-44
We have utilized both molecular dynamics simulations and solution biophysical measurements to investigate the rescue mechanism of mutation N235K, which plays a key role in the recently identified global suppressor motif of K235/Y239/R240 in the human
Publikováno v:
Biophysical Journal. 97(2):554-562
The wide use of lattice-sum strategies in biomolecular simulations has raised many questions on potential artifacts in these strategies. One interesting question is the artifacts in the counterion distributions of highly charged systems. As one would
Publikováno v:
Biophysical Journal. 95:5037-5047
Amyloidlike fibrils are found in many fatal diseases, including Alzheimer's disease, type II diabetes mellitus, transmissible spongiform encephalopathies, and prion diseases. These diseases are linked to proteins that have partially unfolded, misfold
Publikováno v:
The Journal of Physical Chemistry B. 112:7675-7688
We have developed and tested a complete set of nonbonded parameters for a continuum polarizable force field. Our analysis shows that the new continuum polarizable model is consistent with B3LYP/cc-pVTZ in modeling electronic response upon variation o
Publikováno v:
Acta Crystallographica Section D: Biological Crystallography
The impact of hotspot mutation R282Q on the structure of human p53 DNA-binding domain has been characterized by X-ray crystallography and molecular-dynamics simulations.
Tumor suppressor p53 is a sequence-specific DNA-binding protein and its cen
Tumor suppressor p53 is a sequence-specific DNA-binding protein and its cen
Publikováno v:
The Journal of Physical Chemistry B. 111:11538-11545
We have studied room-temperature structural and dynamic properties of the p53 DNA-binding domain in both DNA-bound and DNA-free states. A cumulative 55 ns of explicit solvent molecular dynamics simulations with the particle mesh Ewald treatment of el