Few things serve as the basis of what made me want to do this project. I originally have worked on previous Covid19 projects, which made me know where to look for the source data. Also, I was planning to do something with oddt (The Open Drug Discovery Toolkit), however with latency issues, the project "became" something else.
What it does
The solution is simple, I converted the the source pdb file to a sequence file compatible with SWISS-MODEL's software then created a repository and template for exploration results. More details can be explained via the video I made.
How I built it
I used the WHAT IF Web Interface originally planning to convert the pdb to a FASTA file to look at the protein stands and alignments. However, instead the pdb file was converted to a sequence.pir which I had to remove "illegal characters" to make it compatible with SWISS-MODEL.
Challenges I ran into
It was mainly trial and error. I had problems with oddt, so couldn't use it. Also the original protein I was trying to view with SWISS-MODEL didn't have any template files, so I was lucky to find that 6NB7 didn't have compatibility issues for round #2. I have experience with biostatistics, FASTA files, and all sorts of genomic file formats, so the whole process wasn't too difficult to me. I was originally going to quit because I was waiting two+ hours to see if round #2 would validate or get an error. It validated.
Accomplishments that I'm proud of
This was an extremely simple project, that didn't take that much time. It was more of for me to take a break, so it felt good at least getting something done. I learned alot, and I think this can be quite helpful for researchers and computational biologist to look at. I think I might even have a shot at getting some sort of recognition, who knows?
What I learned
I learned alot about the PDB conversion, sequencing, and templating
What's next for Covid19-Inspired Drug Discovery Toolkit
Not quite sure yet, wanna see how the general public responds to tools like this. Perhaps some consumer discovery or add this with the rest of what I have built.
Model Report References:
- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
- Guex, N., Peitsch, M.C., Schwede, T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis 30, S162-S173 (2009).
- Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
- Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).