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#
By given protein sequences in fasta format, you can run command
> run_local.sh *.seq
to obtain predicted secondary structure, ASA, backbone torsion angles.
##
If you already have pssm files for your proteins.
> run_pssm.py *.pssm
The output will be seen in *.spd3

Reference:
1.	R. Heffernan, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma, J. Wang, A. Sattar, Yuedong Yang* and Y. Zhou*. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. Scientific Reports 2015; 5:11476  
2. R. Heffernan, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma, J. Wang, A. Sattar, Y. Zhou* and Yuedong Yang*. Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinformatics 2016; 32(6):843-9.

If you have any questions, please email to yuedong.yang@gmail.com