Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
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DOI：
10.1021/jp040329x
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发表时间：
2004-10
影响因子：
3.3
通讯作者：
S. Ołdziej;Justyna Ła̧giewka;A. Liwo;C. Czaplewski;M. Chinchio;M. Nanias;H. Scheraga
中科院分区：
文献类型：
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作者：
S. Ołdziej;Justyna Ła̧giewka;A. Liwo;C. Czaplewski;M. Chinchio;M. Nanias;H. Scheraga
我们报告了在所附论文中描述的蛋白质势能景观的分层优化方法的应用（Liwo，A.; Arlukowicz，P.; Oldziej，S.; Czaplewski，C.; Makowski，M.; Scheraga，H. A.物理化学杂志B 2004，108，16918; Oldziej，S.; Liwo，A.; Czaplewski，C.; Pillardy，J.; Scheraga，H. A. J. Phys. Chem. B 2004，108，16934）同时使用两种[1 E0 G（α + β）和1 E0 L（β）]、三种[1 E0 G、1 E0 L和1GAB（α）]以及最后四种训练蛋白[1 E0 G、1 E0 L、1GAB和1 IGD（α + β）]来优化UNRES势能函数;这些训练集和所得到的力场分别被称为2 P、3 P和4P。1 E0 L和1GAB的层次结构是按照应用于1 E0 G的程序确定的，该程序在随附的论文中描述，2 1 IGD和1 E0 G的层次结构分别取自实验和随附的论文2。对于所有的训练集，优化是成功的;换句话说，（i）目标函数组成的con.
We report the application of the hierarchical optimization method of protein potential-energy landscapes described in the accompanying papers (Liwo, A.; Arlukowicz, P.; Oldziej, S.; Czaplewski, C.; Makowski, M.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16918; Oldziej, S.; Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16934) to optimize the UNRES potential energy function using two [1E0G (α + β) and 1E0L (β)], three [1E0G, 1E0L, and 1GAB (α)], and, finally, four training proteins [1E0G, 1E0L, 1GAB, and 1IGD (α + β)] simultaneously; these training sets and the resulting force fields are referred to as 2P, 3P, and 4P, respectively. The hierarchies of 1E0L and 1GAB were determined following the procedure applied to 1E0G described in an accompanying paper,2 the hierarchies of 1IGD and 1E0G being taken from experiment and from the accompanying paper,2 respectively. For all training sets, optimization was successful; in other words, (i) the target function composed of con...