Is it possible to search the sequence space and calculate the energy terms on a amino acid sequence level?

Question

[Neha shri]

Hello everyone,

I am doing my thesis on Protein design. I have generated a database of sequences with some programming. Now I am unable to figure out how to select sequences which will fold into the native structure. Please point me towards how to proceed. Will really be grateful.

Answer 1

[Michael]

Run them through I-Tasser with or without pre-selecting the native structure as template. Potentially, using only parts of the pipeline, like LOMETS and TM-score might do in this case.

[Neha shri]

Thank you for your response.

I have a total of 10 k sequences ,is it feasible to check all of their fold -ability through i tasser or is there some criteria i can filter them out and then go for structure prediction?

[Michael]

You need to filter by sequence similarity (blast) then, potentially by domain presence, annotate you sequences using local InterProScan installation. You cannot possibly hope to run 10k seqs through I-Tasser in reasonable time (takes few days per sequence). Or you need to install I-Tasser locally and run all on a super computer.