I think maybe I can calculate it based on one of the amino acids, such as glysine.
This isn't very accurate but you can estimate if you take the IEP of the sidechains, then work down your peptide chain averaging 7 amines at a time assigning the value to the 4th amine of each average.
You then need to do the same for hydrophobicity (various values for this, be careful) to predict what amines will actually be interacting with water molecules to become charged.
Plot all this data, including your original sidechain values on to a line graph so you can predict localised IEPs and eliminate regions which are less likely to become charged.
This does not take into account any non-linear interactions or post transcriptional modifications so best to compare your predicted values (hydrophobic regions) with crystallography data.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools