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JL2021MD / PROTACModeling

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Occupancy Score and T Score #1

Open wxfsd opened 2 years ago

wxfsd commented 2 years ago

Where are the codes for Occupancy Score and T Score?

JL2021MD commented 2 years ago

This step is not automated so far for the work in the paper, because the slower step is running the MD, while from that data output (processed by cpptraj, giving 10 RMSD plots, then combined into 1 file by "paste" command), it only takes a minute in excel with a saved template to generate the occupancy score for each pose scored, and a few more minutes to count the T score. For larger amounts of data, an automated script will help, and will welcome any input here to constantly update this repository.

JL2021MD commented 2 years ago

Good news! The calculations of the Occupancy Scores and Temperature Scores are now automated. The calculation script is included as part of the QuickStartExample (https://github.com/JL2021MD/PROTACModeling/tree/main/QuickStartExample, https://github.com/JL2021MD/PROTACModeling/blob/main/QuickStartExample.zip).

The actual python script (HAPOD.py) to calculated the values are embedded at the end of the heat.sh shell script, which will calculate those scores for the single MD run after it finishes. Then, the average of 10 runs, along with the standard deviations and errors are calculated by stat.py embedded in https://github.com/JL2021MD/PROTACModeling/blob/main/QuickStartExample/7.getScores.sh.

Please also check out the newly uploaded QuickStartExample, which provides an example project for you to go through the HAPOD scoring in about 15 minutes.