Issue with number of batches

[aribasidd31]

What will be the difference (In backbone diversity or fold) if i generate 1000 backbones in single go or i run it in batches (Ex - 10 batches of 100 backbones? Will it repeat the same folds in all batches or will it produce different folds considering the folds generated in previous batches?

[rclune]

There should be no difference in the diversity of the folds and there is no mechanism for it to produce different folds considering the folds generated in previous batches. Each design is unaware of the other designs in the run.

The only thing to keep in mind that might be relevant is that if you are designing proteins of random lengths, all of the designs in a single batch will be the same length (in terms of number of residues) because the random length is determined for the whole batch.

[aribasidd31]

So that it means that there is possibility that it might generate repetitive folds in different batches?

[rclune]

It is highly unlikely that two structures will be exactly the same, but yes you might see similarities between the secondary structures in your designs. Especially if the constraints you are applying make certain motifs more likely.