Protein Conformation Modeling

Question

I'm interested in learning about computational modeling in biophysics. I have heard some amount about people modeling proteins as a network of ideal springs to examine things like conformation switching. I was thinking it would be cool to try to make a very simple model of a small motif undergoing denaturation at certain temperatures while being stable at others.

Does anyone know of a good reference about protein modeling that would be understandable to someone who is decent with math/physics/programming but is in no way a mathematician/physicist/computer scientist?

Also, if you have a better idea of a simple project for me to practice computational modeling in biophysics (or even just any biology) I would appreciate hearing it.

Thanks

Answer 1

Well I sometimes use PDB files from proteins whose structure has been identified and study them. I use swiss PDB viewer software to do this and its pretty neat! I haven't looked at the biophysical data associated with a PDB file but I'm pretty sure they are there since you wouldn't be able to make the calculations and resolve the protein structure and confirmation without that kind of data. All you need is to download the software, go to Uniprot database and use the accession number of a protein you are interested in, see if its structure is resolved and either download the PDB file or use the accession number to download the file inside the software.