BindProfX Linux tool set-up (2024)

[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 Upon download, I read the README, which appears a bit outdated.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.

[zcx@umich.edu]

The BindProfX tool was last updated in 2017 but its standalone tool should still work fine.

[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.

[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?

[zcx@umich.edu]

No, BindProfX is single threaded.

[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)]

[zcx@umich.edu]

The 0.75/0.25 weights are for FoldX3. 0.9/0.4 weights are for FoldX4 or later.