I have just started out my work in a computational protein design lab.
The first algorithm I learned at the beginning was backrub, which I know basically could be used for flexible backbone design.
After using it for a while, I have some doubt in my mind.
Would you mind sharing your valuable experience on the following situations regarding backrub?
1) I have generated 50k structures by backrub.
After removing redundant sequences, the number of unique amino acid sequence was just 1k.
There was a wide variability of the redundancy of the sequence (i.e. sequence A -> 10k structures, sequence B -> 1k structure, sequence C -> 1 structure)
Assuming I want to find the best sequence which gives rise to the most stable energy score, how would you analyze the result?
Do you just consider the best energy score of each unique sequence or do a statistics of the population of structures generated per sequence?
2) Could I force backrub not to generate structures with redundant sequences?
3) Is it a bad idea if I use backrub to design interface? My idea is : initial pose by docking -> backrub to generate sequence variation -> analyze sequence-binding energy correlation -> (iterate with backrub, experiment..)
Thank you very much!
You are here
Any backrub expert?