Autodock对接过程中对配体有水合作用的分析及处理方法
本帖最后由 川大-小王 于 2013-1-8 21:53 编辑、、、推荐三篇文献，欢迎高人指点、、、（附件中有索取的AD4_water_forcefield.dat) ）
（1）A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking
（2）Exploiting Ordered Waters in Molecular Docking
（3）Molecular Docking with Ligand Attached Water Molecules
Hi Tai-Jin
Prof. Olson forwarded me your request about our hydrated docking method.
First of all thanks for your interest in our publication.
Attached you can find the files required to apply the method to your dockings, including
some example files and the README documentation.
This implementation requires a certain degree of familiarity with the standard AutoDock
protocol and a bit of the command-line interface.
Be aware that with this implementation of the method, it is difficult to compare results
obtained with very diverse ligands without doing some kind of post-processing on the
results, because the energy estimation needs to be normalized. For this reason, the method
is no suitable for virtual screenings. This doesn't affect the structural accuracy, so
docked poses are OK.
There is a rudimentary normalization procedure in the post-processing script ('dry.py',
see documentation) but I'm still working on a better scoring equation, and I wouldn't
recommend to trust values obtained with this method.
If you find any bugs, please report them.
Happy dockings!
Stefano
--
Stefano Forli, PhD
Staff Scientist
Molecular Graphics Laboratory
Dept. Molecular Biology,MB-112F
The Scripps Research Institute
10550North Torrey Pines Road
La Jolla,CA 92037-1000,USA.
tel: (858) 784-2055
fax: (858) 784-2860
email: forli@scripps.edu
http://www.scripps.edu/~forli/
非常谢谢 谢谢分享，很有用
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