Zobrazeno 1 - 10
of 16
pro vyhledávání: '"Meng-Juei Hsieh"'
Publikováno v:
The Journal of Physical Chemistry B. 116:7999-8008
As an integrated step towards a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizab
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5f766db0d6ce525f351be748e0a890d2
https://doi.org/10.1021/jp212117d
https://doi.org/10.1021/jp212117d
Publikováno v:
The Journal of Physical Chemistry B. 116:7088-7101
In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4d2518bad341f6c65896672c866d4f67
https://doi.org/10.1021/jp3019759
https://doi.org/10.1021/jp3019759
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
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::29171c69c73c757ea451b1e26f9b8465
https://doi.org/10.1021/jp906701s
https://doi.org/10.1021/jp906701s
Publikováno v:
Journal of Molecular Graphics and Modelling. 22:415-424
We have investigated the sampling efficiency in molecular dynamics with the PB implicit solvent when self-guiding forces are added. Compared with a high-temperature dynamics simulation, the use of self-guiding forces in room-temperature dynamics is f
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::13e2ebc1e5645998f9c387b54a734dc6
https://doi.org/10.1016/j.jmgm.2003.12.008
https://doi.org/10.1016/j.jmgm.2003.12.008
Publikováno v:
Journal of chemical theory and computation. 6(1)
We implemented and optimized seven finite-difference solvers for the full nonlinear Poisson-Boltzmann equation in biomolecular applications, including four relaxation methods, one conjugate gradient method, and two inexact Newton methods. The perform
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0bd4495ca4f4cfd7e73e4847e0f0c444
https://pubmed.ncbi.nlm.nih.gov/24723843
https://pubmed.ncbi.nlm.nih.gov/24723843
Electrostatics plays a crucial role in determining the structures and functions of biomolecules. Implicit solvent models based on the Poisson–Boltzmann (PB) theory have enjoyed numerous successes in a variety of biological applications associated w
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d72845318237b93923911c45badef0ad
https://doi.org/10.1016/b978-0-444-59440-2.00006-5
https://doi.org/10.1016/b978-0-444-59440-2.00006-5
Autor:
Ray Luo, Hongxing Lei, Qin Cai, Junmei Wang, Jie Li, Meng-Juei Hsieh, Piotr Cieplak, Jun Wang, Yong Duan
In the companion paper, we presented a set of induced dipole interaction models using four types of screening functions, which include the Applequist (no screening), the Thole linear, the Thole exponential model, and the Thole Tinker-like (another fo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d946ef49147d8b78127ac37baf316a69
https://europepmc.org/articles/PMC3082585/
https://europepmc.org/articles/PMC3082585/
Autor:
Yong Duan, Peter A. Kollman, Meng-Juei Hsieh, Lijiang Yang, Ray Luo, Piotr Cieplak, James W. Caldwell, Chun Hu Tan, Junmei Wang
Publikováno v:
The journal of physical chemistry. B. 110(26)
We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic ca
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf303da2ebf0971ec2b63d92801dd144
https://pubmed.ncbi.nlm.nih.gov/16805629
https://pubmed.ncbi.nlm.nih.gov/16805629
Autor:
Meng-Juei Hsieh, Ray Luo
Publikováno v:
Proteins. 56(3)
A well-behaved physics-based all-atom scoring function for protein structure prediction is analyzed with several widely used all-atom decoy sets. The scoring function, termed AMBER/Poisson-Boltzmann (PB), is based on a refined AMBER force field for i
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a086a95ce837f32754b28fb5e0150fc
https://pubmed.ncbi.nlm.nih.gov/15229881
https://pubmed.ncbi.nlm.nih.gov/15229881
Autor:
Ta Hsien Lin, Hsin-tzu Liu, Ming-Shi Shiao, Chen-Kuang Liu, Tzu Chun Tang, Chia-Lin Chyan, Fang-Min Lin, Meng-Juei Hsieh, Yi Chen Chen, Hsien-Bin Huang
Publikováno v:
Journal of Biomolecular NMR. 21:287-288
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::72317fabd6437258a790e7b72b5d0b26
https://doi.org/10.1023/a:1012968805525
https://doi.org/10.1023/a:1012968805525