Please help me, I am working on a protein so i want to know the secondary structure % and what is minimum % of secondary structure should be there to accept the data.
It all depends on what type of protein you have. Make sure you subtract the ellipticity of the sample protein from the buffer. For example, I did a run of BSA and got the secondary structure prediction as 68.44% (alpha-helix) and 8.56% (beta strand) which is kind of incorrect as it should have reported 100% for BSA (BSA has no beta strands).
The output from K2D3 will suggest how much error does the data have and you have to rely on that and make some decisions. If it is an unknown protein, make sure to perform other analytical tools to help contribute to the identity.
thank you for your reply. please let me know the other analytical tools. can you please suggest me.
Other analytical techniques such as FTIR and analyzing the Amide-I band or Dynamic Light Scattering in addition to DSC. I have not performed these but you can try.
I am sorry I wasn't clear on the unknown protein part. By other analytical tools I meant combining the data obtained from say LC-MS and digesting it with proteolytic enzyme such as Trypsin and mapping the peptides and hope that you can compare it to a database if one exists for that.
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