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README.md

@@ -35,38 +35,37 @@ As to where the dataset comes from in this broader work, the relevant dataset (#
 
 ## Sample Protein Stability Data
 
-| Base Protein Sequence                                      | Mutation | ΔΔG_ML            | Classification |
-|------------------------------------------------------------|----------|--------------------|----------------|
-| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK            | base     | -0.0675543480388345| neutral       |
-| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK            | D1Q      | -0.0162349479755414| neutral       |
-| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK            | D1E      | -0.1402534094665108| neutral       |
-| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK            | I3K      | -0.6219710162367509| stabilising   |
-| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK            | I3W      |  0.6204920350860421| destabilising |
-
+| Base Protein Sequence                                       | Mutation | ΔΔG_ML             | Classification  |
+|-------------------------------------------------------------|----------|--------------------|-----------------|
+| FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL | R63W    | -0.2010871345320799 | neutral        |
+| FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL | R63Y    |  0.0194756159891467 | neutral        |
+| FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL | R63F    |  0.7231614929744659 | stabilising    |
+| FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL | R63P    | -0.3668887752897785 | neutral        |
+| FDIYVVTADYLPLGAEQDAITLREGQYVEVLDAAHPLRWLVRTKPTKSSPSRQGWVSPAYLDRRL | R63C    | -0.5317304030261774 | destabilising  |
 
 ## Dataset Structure
 
-The dataset focuses on the differential deltaG (mutation minus base) of various protein mutations.
+The dataset focuses on the differential deltaG of *unfolding* (mutation minus base) of various protein mutations.
 
 - **Base Protein Sequence** (`aa_seq`): A (sometimes shortened) amino acid sequence.
 - **Mutation**: Represented as a combination of amino acid and its position (e.g., F10N indicates changing the 10th amino acid (F) in a sequence for N).
-- **delta deltaG** (`ddG_ML`): Derived from a model that makes use of stability measurements measured by two proteases, trypsin and chymotrypsin.
-- **Classification**: Classification is done purely on the basis of ddG. The standard deviation of ddG in the dataset is measured and:
--- Rows above 0.5 standard deviations are classified as 'destabilising'
--- Rows below -0.5 standard deviations are classified as 'stabilising'
+- **delta deltaG** (`ddG_ML`): Derived from a model that makes use of stability measurements (free energy of unfolding) measured by two proteases, trypsin and chymotrypsin.
+- **Classification**: Classification is done purely on the basis of ddG.
+-- Rows below -0.5 standard deviations are classified as 'destabilising'
+-- Rows above +0.5 standard deviations are classified as 'stabilising'
 -- Rows between -0.5 and 0.5 standard deviations are classified as 'neutral'
   
 ### Understanding ΔG (delta G)
 
 ΔG is the Gibbs free energy change of a process, dictating whether a process is thermodynamically favorable:
 
-- **Negative ΔG**: Indicates the process is energetically favorable. For protein folding, it implies the protein is stable in its folded form.
-- **Positive ΔG**: Indicates the process is not energetically favorable. In protein folding, it means the protein requires energy to maintain its folded state.
+- **Negative ΔG**: Indicates the process is energetically favorable. For protein unfolding, it implies the protein is more stable in its unfolded form.
+- **Positive ΔG**: Indicates the process is not energetically favorable. In protein unfolding, it means the protein requires energy to maintain its unfolded state, i.e. it is stable in folded form.
 
 The **delta delta G** (ΔΔG) represents the deltaG of the mutation compared to the base protein:
 
-- **Positive ΔΔG**: Suggests the mutation decreases protein stability.
-- **Negative ΔΔG**: Suggests the mutation enhances protein stability.
+- **Positive ΔΔG**: Suggests the mutation enhances protein stability.
+- **Negative ΔΔG**: Suggests the mutation decreases protein stability.
 
 ### Data Cleanup and Validation: