Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
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DOI：
10.1016/s0969-2126(03)00186-2
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发表时间：
2003-09-01
期刊：
影响因子：
5.7
通讯作者：
van Aalten, DMF
中科院分区：
文献类型：
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作者：
Kleywegt, GJ;Henrick, K;van Aalten, DMF
对于蛋白质和核酸结构的精化，可以使用高质量的几何约束库。不幸的是，对于其他化合物，例如生理配体、先导化合物、底物类似物等，情况并不那么有利。因此，在生物大分子复合物中发现的小分子结构通常不如周围的氨基酸或核酸可靠。在这里，我们简要回顾了几何约束在结构细化（无论是针对 X 射线晶体学还是核磁共振衍生数据）和模拟中的使用。此外，我们讨论了生成小分子约束库和（理想化）坐标的方法，并提供了一些实用的建议。
For the refinement of protein and nucleic acid structures, high-quality geometric restraint libraries are available. Unfortunately, for other compounds, such as physiological ligands, lead compounds, substrate analogs, etc., the situation is not as favorable. As a result, the structures of small molecules found in complexes with biomacromolecules are often less reliable than those of the surrounding amino or nucleic acids. Here, we briefly review the use of geometric restraints in structure refinement (be it against X-ray crystallographic or NMR-derived data) and simulation. In addition, we discuss methods to generate both restraint libraries and (idealized) coordinates for small molecules and provide some practical advice.