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README.md

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-# Protein Data Stability
+# Protein Data Stability - Single Mutation
 
+This repository contains data on the change in protein stability with a single mutation.
 
+## Attribution of Data Sources
 
-## Attribution of data sources
+- **Primary Source**: Tsuboyama, K., Dauparas, J., Chen, J. et al. Mega-scale experimental analysis of protein folding stability in biology and design. Nature 620, 434–444 (2023). [Link to the paper](https://www.nature.com/articles/s41586-023-06328-6)
+- **Dataset Link**: [Zenodo Record](https://zenodo.org/record/7992926)
 
+## Sample Protein Stability Data
+
+| Base Amino Acid Sequence                                                   | Mutation | ddG_ML                 | Classification |
+|---------------------------------------------------------------------------|----------|------------------------|----------------|
+| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK                            | base     | -0.0675543480388345    | neutral        |
+| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK                            | D1Q      | -0.0162349479755414    | neutral        |
+| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK                            | D1E      | -0.1402534094665108    | neutral        |
+| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK                            | D1N      | 0.0126650189159422     | neutral        |
+| DEIHIHFNGVTIEFRGLTEEAKKALEEAIKRGASEEELKELARRLIK                            | D1H      | 0.1970434798619962     | neutral        |
 
 ## Dataset Structure
 
+The dataset focuses on the differential deltaG (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.
+  
+### 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.
+
+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.
+
+### Dataset preparation:
+
+For a quick overview, the relevant dataset structure can be found in `dataset_table.jpeg`.
+
+### Data Cleanup and Validation:
+
+1. Filtering: The dataset has been curated to only include examples of single mutations.
+2. Consistency Check: Only rows with consistent mutation indication, aligned with both the base and mutated sequences, have been retained.