# ProteoCast prediction results

This folder contains the output files generated by a **ProteoCast** analysis
for a single protein sequence.

---

## Files

### 1. `XXXX.fasta`
Reference amino-acid sequence used for the analysis and provided to generate
the Multiple Sequence Alignment (MSA).

---

### 2. `aliXXXX.fasta`
Multiple Sequence Alignment used for evolutionary inference.
The alignment can be retrieved from the AlphaFold Database or provided by the user
and is reformatted to FASTA when necessary (e.g. from A2M/A3M formats).

---

### 3. `XXXX_msaRepresentation.jpg`
Graphical representation of MSA coverage and residue conservation along the sequence.

---

### 4. `XXXX_ProteoCast.csv`
Main ProteoCast output containing predicted effects for **all possible single amino-acid substitutions**.

Each row corresponds to one mutation and includes the following fields:

- **Mutation**  
  Amino-acid substitution in one-letter code (e.g. `M1A`).

- **Variant_score**  
  Predicted impact score for the variant.  
  More negative values indicate stronger deleterious effects.

- **Residue**  
  Position of the mutated residue in the input sequence (1-based indexing).

- **LocalConfidence**  
  Boolean flag indicating whether the residue is located in a region with
  sufficient evolutionary signal for reliable prediction.

- **Variant_class**  
  Qualitative classification of the variant effect (e.g. `neutral`, `mild`, `impactful`).

- **Residue_class**  
  Classification of the residue as `sensitive` or `tolerant`, based on the
  distribution of variant scores at this position.

- **pdb_pos** *(if structural information is used)*  
  Corresponding residue index in the reference structure
  (empty if unmapped).

- **RSA*Variant_score**  
  Structure-informed score obtained by weighting the **Variant_score**
  by the relative solvent accessibility (RSA) of the wild-type residue.
  Empty when structural information is unavailable.

- **aligned**  
  Boolean flag indicating whether the residue is covered by the structure alignment.

---

### 5. `XXXX_MutLand.jpg`
Mutational landscape summarizing the predicted effect of all substitutions
across the protein sequence.

---

### 6. `XXXX_GMM.jpg`
Gaussian Mixture Model visualization used to classify residues according to
their mutational sensitivity.

---

### 7. `mutants.txt` *(optional)*
List of user-provided mutations, optionally associated with experimental or
phenotypic information.

---

### 8. `XXXX_Segmentation.csv`
Segmentation of the protein sequence into contiguous regions based on
mutational sensitivity profiles.

Each row corresponds to one segment and includes:
- **start** (inclusive)  
- **end** (inclusive)  
- **mean** mutational sensitivity score over the segment  
- **state** (0, 1, 2), reflecting increasing levels of mutational sensitivity  
- **type**, indicating the metric used for segmentation (`GEMME` or `pLDDT`)  
- **protein**, identifier of the analyzed protein  

Segmentation is provided both for mutational sensitivity (GEMME) and,
when available, for AlphaFold confidence (pLDDT).

---

### 9. `XXXX_SegProfile.png`
Visualization of the segmentation profile along the protein sequence.

---

### 10. `XXXX.pdb` *(optional)*
Reference 3D structure used for structure-informed analyses.

---

### 11. `XXXX_ResClass.pdb` *(optional)*
Structure with residue class (`sensitive` / `tolerant`) encoded in B-factors.

---

### 12. `XXXX_Sensitivity.pdb` *(optional)*
Structure with average mutational sensitivity encoded in B-factors.

---

### 13. `XXXX_ResRSA.pdb` *(optional)*
Structure with relative solvent accessibility (RSA) encoded in B-factors.

---

### 14. `XXXX_GEMME_pLDDT.csv`
GEMME evolutionary scores combined with AlphaFold pLDDT confidence values
(when structural information is available).

---

### `mapping_fasta_pdb.csv`
Mapping between sequence positions and structure residue indices.

---

### `rsa_values.csv`
Computed relative solvent accessibility (RSA) values for all residues in the structure.

---

## Directories

### `GMM/`
Contains detailed outputs related to the Gaussian Mixture Model.

### `XXXX/`
Contains intermediate and auxiliary files generated by GEMME during
variant effect prediction.

---

## Notes

- Variant effect scores are **protein-specific** and should not be compared
  across different proteins.
- Structure-informed annotations depend on the provided structure and
  sequence–structure mapping.

For more information, see the documentation:  
https://proteocast.ijm.fr/documentation
