Comparison of protein structures

Question

[lochanamp]

For my undergraduate research project i'm trying to compare the structures of some proteins, specifically transcription factors crucial for dehydration tolerance in plants, in the hope of finding differences that make each protein more or less dehydration tolerant than the others. Is there any database or a site where i can find information regarding this?

[Kevin Blighe]

I believe that Jmol has an algorithm (or algorithms) that allow you to compare proteins. This is certainly possible, visually, with Jmol, and one can even infer hydrogen bonds, di-sulfide bonds, and van der Vaal's interactions with it.

Have you had much success since you made your post?

I noticed that no-one had replied, so, I felt obliged to help.

Kevin

Answer 1

[fileyfood]

You can start by visualizing protein structures in a variety of different tools, including offline tools like PyMOL (has an online version as well), VMD, and many web tools using MolStar (e.g. the G2P portal).

You can get secondary structure information using DSSP, and pocket information using SiteMap or fpocket (which is open source).