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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >Ligand identification using electron-density map correlations
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Ligand identification using electron-density map correlations

机译：配体识别使用电子密度图相关性

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摘要

A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F-o-F-c) exp(i phi(c)) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.
机译：配体的识别过程晶体结构的大分子描述。对应于一个配体中使用识别过程。配体的密度与每一组测试配体后优化的配合配体的密度。指纹的密度的相关性模型密度的指纹可能的配体。有序列表的每个测试的相关性配体的密度。使用z分数得分的方法吗相关性是均值和规范化标准偏差的相关性发现各种各样的不匹配ligand-density双,所以的Z分数与概率有关观察的一个特定的值相关的机会。一组200最常见配体的蛋白质数据银行,集体代表57%的配体的蛋白质数据银行。配体密度的特点,排名列表为配体的识别代表(F-o-F-c) exp(我φ(c))的区别密度的条目蛋白质数据银行。48%的200例病例中,正确的配体配体的排名列表的顶部。在识别方法可能是有用的未知的新大分子配体结构以及配体的识别在已绑定到一个高分子混合物。

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