How to acheive Combinatorial optimization in case of protein sequences?

Question

[Neha shri]

I am working on Inverse Protein Folding Problem

I have created a database of protein sequences, in which every sequence is identical to its native sequence up to 65%, I need to select sequences that can fold into the native structure.

Is there any algorithm that can solve this optimization problem and which computer language is it suitable to implement it. Any pointers will be appreciated.