What is SOuLMuSiC?
SOuLMuSiC is a computational tool that, given a protein structure, predicts the impact of all possible single-site amino acid substitutions on protein solubility. It is based on a simple shallow artificial neural network that takes as input a series of features, including the biophysical properties of the wild-type and mutated residues, energetic values computed using various statistical potentials, and mutational scores derived from protein language model approaches.
How to Submit a Query to SOuLMuSiC
Running SOuLMuSiC is very simple and only requires a protein structure as input. Users can provide either:
-
A 4-letter code of a PDB structure, which is then automatically downloaded from the
Protein Data Bank.
-
A UniProt ID, for which we will download the corresponding
AlphaFoldDB structure.
-
A personal PDB file (.pdb).
After clicking on the Submit button, you will be prompted to select the type of structure you are submitting, whether it is a globular protein or a large insoluble macromolecular assembly (such as fibrils).
Recommendation: We suggest users to provide protein structures corresponding to biological units, including all the chains in the native structure. This is particularly important for homomultimers.
The results of SOuLMuSiC will be sent to your academic email. Depending on the protein's length, results may take anywhere from
one to a few minutes. Please note that each user can only run
one protein at a time.
SOuLMuSiC is free to use for academic users only, and thus requires an academic email address.
For commercial use or in case of any problem, please contact us (Marianne.Rooman@ulb.be or
Fabrizio.Pucci@ulb.be).
SOuLMuSiC results and interpretation
SOuLMuSiC returns a .dat file containing the predicted fitness scores of all single-site amino acid substitutions of the protein. The columns in the file contain:
- Columns 1-5: Information about the mutations.
- Columns 6: Residue Solvent Accessibility (RSA) of the mutated residue.
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Columns 7: The SOuLMuSiC score that estimates how solubility changes upon mutations. A score around of +2 or +1 indicate mutations that strongly or slightly increase solubility, respectively. A score close to zero means there is no significant change in solubility. A score around -1 indicates a mild negative impact on solubility, while scores of -2 or below indicate a strong negative effect caused by the mutations.
Do not hesitate to contact us at
Marianne.Rooman@ulb.be or
Fabrizio.Pucci@ulb.be. Feedback is more than welcome.
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