Experiments in Applying TDA Towards Proteins

Credits

• Stack Overflow user "The fourth bird"'s code for extracting entries from .sdf files
• The compounds that Proline was compared against (Proline analogs) are obtained from "Independence of Proline Chemotaxis and Transport in Bacillus subtilis"(Ordal et al.)
• the Choice of Galectin-1 as a protein was taken from "Small proteins: untapped area of potential biological importance" (Su et al). which is highlighted for it small size
• .sdf files were taken from PubChem
• Conversion of .sdf's to .pdb's was done with Open Babel
• Some experimentation was done in generating distance matrices using scipy

Structure

• Failed-tmscoring.ipynb - An early failed attempt to compare Proline with Azetidine-2-COOH
• Ripser-SDF.ipynb - Applications of Ripser on Proline analogs
• Galectin-1.ipynb - Attempt to apply Ripser on the Galectin-1 protein, failed due to resource consumption
• Galectin-1-GUDHI.ipynb - Attempt to apply GUDHI in creating a Rips Complex and getting persistence data, failed due to resource consumption