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cfmzxf84

木虫 (正式写手)

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[求助] 关于GOLD和autodock的打分函数和自由能计算

请教，我进行小分子和酶的对接，对文献已经测定了晶体结构的配合物进行redocking，GOLD的重合度要高于autodock的
但是，GOLD的打分函数好像和能量之间的关系不是很好。我想看看小分子和酶的binding affinity
想问下，GOLD的打分函数和能量之间的关系如何？看官网说
GOLD has been optimised for the prediction of ligand binding positions rather than the prediction of binding affinities. However, we have found that a sub-component of the GOLD scoring function can be more effective, showing a 60% correlation with a test set of known binders. This can be derived from GOLD by summing the external terms of the fitness function. From the rank file of a given ligand, if the results are re-scored using only S(hb_ext) and 1.375 * S(vdw_ext), the correlation with affinity is better than if you use the full score.
S(hb_ext) and 1.375 * S(vdw_ext)是S(hb_ext) +1.375 * S(vdw_ext)吗？还是S(hb_ext) or1.375 * S(vdw_ext)，具体怎么操作呢？谢谢
顺便再请教下GOLD和autodock哪个精度高？哪个文献多？谢谢

[ Last edited by cfmzxf84 on 2012-4-23 at 10:34 ]

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