Entering edit mode
5.4 years ago
I have a bunch of designed protein sequences and I want to assess the quality of their sequence and structure.
what are the best methods of analyzing an amino acid sequence? how to validate it as a native-like protein?
and also after predicting their structure, what are the best ways to analyze the 3D structure of proteins?
Actually, I want to know how good and valid are my designed sequences?
criteria which can validate amino acid sequences and structures both chemically and biologically.
I don’t think such a tool exists. There is very little way to know a priori that a protein will express and fold in reality.
This question is meaningless. You haven’t said what it is you want to ‘analyze’.
It vaguely sounds like you want to do homology modelling.
It sounds like you want to do homology modelling of your sequences. There is an online tool called Rampage, which will give ramachandran plot for your predicted structure and gives the percentage of amino acids present in outlier regions etc.
Also you have an online tool called Prosa, which will compare your predicted protein with all the experimental proteins.