feat: FoldX predicted energies in variant annotation #947
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… into ds_3676_foldx
vivienho
reviewed
Feb 5, 2025
| """ | ||
| return f.when(f.abs(score) >= 5, f.lit(1.0)).otherwise( | ||
| cls._rescaleColumnValue(f.abs(score), 0.0, 5.0, 0.0, 1.00) | ||
| ) |
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From the function documentation I expected that scores above 2 should be normalised to 1, but here it is 5?
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I wanted to be very conservative. Assigning 1.0 score to the most serious free energies, it is especially relevant when talking about the negative energies, which indicates stabilisation. That might be has negative impact on the overall structure/function. The thresholds applied for normalisation were established in a "heuristic" manner. :D
vivienho
approved these changes
Feb 5, 2025
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Context
OTAR2081 mapped the mutational landscape of the full human proteome by systematically changing every amio-acid to all other amino acid in the AlphaFold structures of all human protein. The mutation effect is assessed by the comparing energies of the structures via FoldX. The raw and scaled ddG values are used as
inSilicoPredictorsfor all variants in the variant index that causes the same amio-acid change in the given protein.The PR contains