What is the optimal frame size for protein secondary structure prediction methods?
By frame size, do you mean sliding window?

I know that if you want to predict a secondary structure of a transmembrane protein, then your window size should be 20 amino acids (this is the average length of 1 transmembrane alpha helix spanning through the membrane). 

I found this paper by Chen, Kurgan, and Ruan[1].

It basically says that the window size depends on what kind of pattern you are looking for, but in general, 19 residues should be optimal. 

Also, secondary structure predictors rely on many features like hydrophobicity, missing coordinates in X-ray structures, B-factors, motifs, etc.




Chen K, Kurgan L, Ruan J. 2006. Optimization of the Sliding Window Size for Protein Structure Prediction. CIBCB '06: 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, pp.1-7, 28-29, doi:10.1109/CIBCB.2006.330959.