When You Can't Afford the Software Suite and Won't Trust the Free Website
What do you do as a consultant when you need a software tool that either comes bundled in an expensive suite or lives on some random website?
Pasting a proprietary sequence for the next blockbuster drug into an unknown web tool is not something I am comfortable with. And I cannot justify paying more than $10K for a molecular modeling suite I need for one hour. So I decided to build my own tools, with a little help from Claude.
One of the things I genuinely enjoy about consulting is the flexibility to invest time in projects like this. I have always liked programming, but as a manager in big pharma it was mostly a distraction from what I was actually supposed to be doing. Now I have the time, so I used it.
The result is a suite I call Protein Sequence Tools (PS Tools). All four tools operate on amino acid sequences:
Protein Fragment Mass Calculator: Import a sequence, select a portion of it, and calculate the mass of that fragment. Useful when you are working through intact LC-MS data and trying to identify clipping or truncation products. Supports both average and monoisotopic mass.
Protein Digestor: Select an enzyme, get the masses of all proteolytic fragments. There are plenty of these tools online. I wanted one I could trust.
Protein Aligner: Align two or more sequences and highlight the differences. Particularly useful for comparing related antibodies. Includes a choice of algorithms for CDR identification.
Protein Liability Analyzer: Takes a sequence and flags likely liabilities, glycosylation sites, and other PTMs based on rules from the literature. You can also load a PDB file to bring in the crystal structure and factor in solvent accessibility for each potential hot spot.
Yes, I am aware of the irony. I built my own shady website where you paste your protein sequence. The difference is that I know how it was designed and I know it is secure. The tools are written in JavaScript (I also have Python versions), so you can inspect the source directly in your browser or check the GitHub repository.
But you do not have to take my word for it. If you want a version you can run locally and clear with your IT department, reach out. I can provide an executable or an installer package. I charge for my time, but that is all you are paying for. Give the tools a try and let me know what you think.