Zobrazeno 1 - 5
of 5
pro vyhledávání: '"Mathew C. Lee"'
Characterizing the Rate-Limiting Step of Trp-Cage Folding by All-Atom Molecular Dynamics Simulations
Publikováno v:
The Journal of Physical Chemistry B. 108:13855-13865
In this study, the detailed mechanisms of the rapid-folding Trp-cage mini-protein were investigated by extensive all-atom molecular dynamics simulations of both wild-type and mutant proteins using a recently developed point-charge force field within
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4a764461824439d30540e7a31ad537b6
https://doi.org/10.1021/jp0478920
https://doi.org/10.1021/jp0478920
Autor:
Mathew C. Lee, Yong Duan
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 55:620-634
Recent works have shown the ability of physics-based potentials (e.g., CHARMM and OPLS-AA) and energy minimization to differentiate the native protein structures from large ensemble of non-native structures. In this study, we extended previous work b
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::56e727bec21c91528167e5f27acb30da
https://doi.org/10.1002/prot.10470
https://doi.org/10.1002/prot.10470
Publikováno v:
Journal of Molecular Biology. 327:711-717
Here, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on condensed-phase quantum mechanical c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8db1f4419947b62e309988f52490fd0a
https://doi.org/10.1016/s0022-2836(03)00177-3
https://doi.org/10.1016/s0022-2836(03)00177-3
Autor:
Junmei Wang, Yong Duan, Piotr Cieplak, Wei Zhang, Peter A. Kollman, Shibasish Chowdhury, James W. Caldwell, Ray Luo, Tai-Sung Lee, Guoming Xiong, Rong Yang, Chun Wu, Mathew C. Lee
Publikováno v:
Journal of computational chemistry. 24(16)
Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Corne
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ebe9e8cbc4a816f62f5812f620ae92e
https://pubmed.ncbi.nlm.nih.gov/14531054
https://pubmed.ncbi.nlm.nih.gov/14531054
Autor:
Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman
Publikováno v:
Journal of Computational Chemistry; 2003, Vol. 24 Issue 16, p1999-2012, 14p