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SecundaryStructure Filter

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SecundaryStructure Filter


I have been trying to design using blueprint. After the design, I use the SecundaryStructure filter with the abego set to true, so that in addition to verifying secondary structure, it looks at the torsion angles set. I have been guided by the study "Control over overall shape and size in de novo designed proteins" by Yu-Ru Lin to establish the abego. In my case, I have trouble filtering the abego in the last position; For example, for a peptide of 12 amino acids, when the design passes through the filter that last position 12, which is a loop amino acid, does not happen with any abego, nor with A, B, E or G. I have noticed the torsion angles of that last position shown in the output and always corresponds to a negative phi value, psi is 0 and omega is 0; if I am guided by the study, those values ​​correspond to region A, it still does not pass the filter. I have tried to lengthen that flanking loop with another residue, now it would be 13 amino acids in total, becoming position 13 that of the problem, which does not pass the filter. I hope you can help me, thanks in advance.

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Sat, 2021-11-20 23:41