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tommyhuangthu / EvoEF

a fast and accurate physical energy function for predicting protein stability and protein-protein affinity changes upon amino-acid mutations
MIT License
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Rotamer library #5

Closed jnoske closed 5 months ago

jnoske commented 5 months ago

Is it possible to use a library with more rotamere and does this make the algorithm more accurate?

tommyhuangthu commented 5 months ago

Yes, I think so. There are four rotamer libraries in the EvoEF/library directory: rotlib984.txt, rotlib3222.txt, rotlib7421.txt, and rotlib11810.txt. By default, rotlib984 is used with a balanced accuracy and running speed. You can change the code in EvoEF/src/Main.cpp on line 76: change the rotamer library to the one you want to use, save the file, and recompile the code the generate the EvoEF executable.

Best wishes, Xiaoqiang

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Is it possible to use a library with more rotamere and does this make the algorithm more accurate?

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jnoske commented 5 months ago

Thank you for the help! Is there any information how these different sizes of rotamer libraries where compiled?

tommyhuangthu commented 5 months ago

Hello, You can refer to this paper for information on the rotamer library: https://doi.org/10.1006/jmbi.2001.4865

Best wishes, Xiaoqiang

From: Jakob Noske @.> Sent: Tuesday, March 26, 2024 10:58 To: tommyhuangthu/EvoEF @.> Cc: Xiaoqiang Huang @.>; Comment @.> Subject: Re: [tommyhuangthu/EvoEF] Rotamer library (Issue #5)

Thank you for the help! Is there any information how these different sizes of rotamer libraries where compiled?

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jnoske commented 5 months ago

Thank you!