Derivation of a scoring function for crystal structure prediction
Derivation of a scoring function for crystal structure prediction
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DOI：
10.1107/s0108767301004810
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发表时间：
2001-07-01
期刊：
影响因子：
--
通讯作者：
Lengauer, T
中科院分区：
文献类型：
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作者：
Apostolakis, J;Hofmann, DWM;Lengauer, T
不断增加的实验解决的晶体结构的数量支持的可能性，完全经验的晶体结构预测的小有机分子。经验方法比试图从第一原理解决同一问题的方法要有效得多。然而，从数据到经验知识和进一步的功能算法的转换是不平凡的，结果的有用性在很大程度上取决于数据的数量和质量。在这项工作中，一个简单的评分函数参数化，以区分正确的结构和一组诱饵大量不同的分子系统。该方法是全自动的，其优点是可以立即参数化完整的评分函数，从而产生一组自洽的参数。所得到的评分功能上测试一组独立的晶体结构从P1和P1空间群。使用训练的评分函数和FlexCryst小分子晶体结构预测程序，结果表明，在空间群P1的239个测试分子中，约73%被正确预测。对于更复杂的空间群P1，成功率为26%。与力场电位的比较表明所获得的评分函数的物理内容，直接重要的蛋白质线程的结果，这种基于数据库的电位被应用。
The ever increasing number of experimentally resolved crystal structures supports the possibility of fully empirical crystal structure prediction for small organic molecules. Empirical methods promise to be significantly more efficient than methods that attempt to solve the same problem from first principles. However, the transformation from data to empirical knowledge and further to functional algorithms is not trivial and the usefulness of the result depends strongly on the quantity and the quality of the data. In this work, a simple scoring function is parameterized to discriminate between the correct structure and a set of decoys for a large number of different molecular systems. The method is fully automatic and has the advantage that the complete scoring function is parametrized at once, leading to a self-consistent set of parameters. The obtained scoring function is tested on an independent set of crystal structures taken from the P1 and P 1 space groups. With the trained scoring function and FlexCryst, a program for small-molecule crystal structure prediction, it is shown that approximately 73% of the 239 tested molecules in space group P1 are predicted correctly. For the more complex space group P 1, the success rate is 26%. Comparison with force-field potentials indicates the physical content of the obtained scoring function, a result of direct importance for protein threading where such database-based potentials are being applied.