A hybrid genetic algorithm with pattern search for finding heavy atoms in protein crystals
A hybrid genetic algorithm with pattern search for finding heavy atoms in protein crystals
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一种具有模式搜索的混合遗传算法，用于在蛋白质晶体中寻找重原子
DOI：
10.1145/1068009.1068071
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发表时间：
2005
影响因子：
3
通讯作者：
M. Eppstein
中科院分区：
文献类型：
--
作者：
Joshua L. Payne;M. Eppstein
确定蛋白质分子结构的一种方法是一种被称为同象置换的技术，在这种技术中，晶学家在蛋白质晶体中掺杂重原子，如汞或铂。通过比较含有和不含有重原子的蛋白质晶体X射线衍射的测量幅度，可以估计出重原子的位置。一旦知道了重原子的位置，就可以估计通过蛋白质晶体的X射线的衍射物相，这反过来又可以估计蛋白质的结构。遗憾的是，这一过程中的关键步骤是对重原子位置的估计，这是一个多峰、非线性的逆问题。我们报道了一项初步研究的结果，结果表明，使用阶段1的随机遗传算法和阶段2的确定性模式搜索算法的两阶段混合算法，可以成功地使用无噪声数据在计算机模拟晶体中定位多达5个重原子。我们的结论是，该方法可能是一种在蛋白质晶体中寻找重原子的可行方法，并提出了将该方法扩展到更大问题的方法。
One approach for determining the molecular structure of proteins is a technique called iso-morphous replacement, in which crystallographers dope protein crystals with heavy atoms, such as mercury or platinum. By comparing measured amplitudes of diffracted x-rays through protein crystals with and without the heavy atoms, the locations of the heavy atoms can be estimated. Once the locations of the heavy atoms are known, the phases of the diffracted x-rays through the protein crystal can be estimated, which in turn enables the structure of the protein to be estimated. Unfortunately, the key step in this process is the estimation of the locations of the heavy atoms, and this is a multi-modal, non-linear inverse problem. We report results of a pilot study that show that a 2-stage hybrid algorithm, using a stochastic genetic algorithm for stage 1 followed by a deterministic pattern search algorithm for stage 2, can successfully locate up to 5 heavy atoms in computer simulated crystals using noise free data. We conclude that the method may be a viable approach for finding heavy atoms in protein crystals, and suggest ways in which the approach can be scaled up to larger problems.
用于二十面体病毒从头开始定相的遗传算法。
DOI：
10.1107/s0907444995011620
发表时间：
1996
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Miller,ST;Hogle,JM;Filman,DJ
通讯作者：
Filman,DJ