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

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.

protein-design energy-calculations sequence-space
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updated by Ram Ram • written by Neha shri • Neha shri

1 answer

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.

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written by Michael Dondrup Michael Dondrup

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?

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written by Neha shri • Neha shri

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.

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written by Michael Dondrup Michael Dondrup

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