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BindProfX Linux tool set-up (2024)
Posted: Tue Jan 09, 2024 8:29 pm
by al519
Hi all,
I am attempting to set up the
BindProfX tool for Linux (
https://zhanggroup.org/BindProfX/download/). Upon download, I read the README, which appears a bit outdated. Has anyone set up the BindProfX Linux tool recently? Can you provide a list of what must be done for complete installation?
Thank you.
Re: BindProfX Linux tool set-up (2024)
Posted: Wed Jan 10, 2024 2:37 am
by zcx@umich.edu
The BindProfX tool was last updated in 2017 but its standalone tool should still work fine.
Re: BindProfX Linux tool set-up (2024)
Posted: Wed Jan 10, 2024 2:53 pm
by al519
Thank you for getting back to me. I understand the tool should work fine, but I'd like to know whether the instructions in the README are up-to-date because they appear not to be. I want to set up the BindProfX tool as intended, and I would appreciate clarification if its current README is exhaustive and up-to-date.
Re: BindProfX Linux tool set-up (2024)
Posted: Wed Jan 10, 2024 6:53 pm
by al519
I am in the process of testing it right now. On another note, can any of the BindProfX scripts take advantage of multiple CPU cores or, better yet, GPUs?
Re: BindProfX Linux tool set-up (2024)
Posted: Sun Jan 21, 2024 2:15 am
by zcx@umich.edu
No, BindProfX is single threaded.
Re: BindProfX Linux tool set-up (2024)
Posted: Thu Jan 25, 2024 7:48 pm
by al519
I noticed the formula for the final weighted score has changed. Are the 0.75/0.25 weights better than the 0.9/0.4 weights?
Here is the relevant code:
Code: Select all
#FinalScore_list=[x if ',' in m else 0.9*x+0.4*f for x,f,m in \
#zip(XProfScore_list,FoldXScore_list,mutation_list)]
FinalScore_list=[0.75*x+0.25*f for x,f,m in \
zip(XProfScore_list,FoldXScore_list,mutation_list)]
Re: BindProfX Linux tool set-up (2024)
Posted: Tue Jan 30, 2024 2:51 pm
by zcx@umich.edu
The 0.75/0.25 weights are for FoldX3. 0.9/0.4 weights are for FoldX4 or later.