Free and Secure Protein Sequence Tools

Here is a collection of tools that I developed for my own work doing protein mass spectrometry for many years. I am happy to share them for anybody to use as is. They were designed with privacy in mind so the sequences pasted remain private. All processing is done locally on your computer. For commercial use, please contact me to purchase a stand-alone copy that you could host on your computer. I can also modify them to suit your particular needs.

Protein Fragment Mass Calculator. This software works on a user-provided amino acid sequence and calculates the mass of the selected fragment. It can calculate average or monoisotopic mass.

Protein Digestor. This software works on a user-provided amino acid sequence lets the user select a digestion enzyme and calculates the mass of the all the proteolytic fragments.

Protein Aligner.This software aligns two or more protein sequences.

Protein Liability Analyzer. This software takes a protein sequence and identifies hot spots, glycosylation sites based on the primary sequence. You can also include a PDB file and it will take into account the higher order structure of the protein and solvent availability of each potential hot spot.