I am currently doing my Masters in Physics, and I am planning to start my Thesis this summer on Protein Folding in Biophysics. It would be great help if anyone could suggest me or give me proper direction to start with like any programs to use, programming language to learn or any papers to read.
What are you going to do exactly? If you want to predict secondary structure by converting psi/phi/omega angles you should look at this site http://www.netcomuk.co.uk/~jenolive/vect14.html and this paper explains a lot about secondary structures etc
Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features by Wolfgang Kabsch and Christian Sander
onlinelibrary.wiley.com/doi/10.1002/bip.360221211/pdf
If you are going in deeper, to actual complete protein modeling, this is a homology driven protein folding program we used at one of our courses http://www.salilab.org/modeller/tutorial/basic.html
A paper that discusses the pro's and con's of this type of folding prediction is;
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. by Lucy R. Forrest, Christopher L. Tang, and Barry Honig http://www.ncbi.nlm.nih.gov/pubmed/16648166
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