Table 3 Comparison of runtime between DALI and Protein-Vec for searching 73 SCOPe domains against the full clustered AFDB

From: Functional protein mining with conformal guarantees

Method

Runtime

Number of threads

DALI

~ 1 day

10

Protein-Vec

~ 30 seconds

1

  1. Given the substantial speed difference between Protein-Vec and prior methods, prefiltering reference databases before structural alignment can significantly reduce computational costs.
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