“Assessment of the Fragment Docking Program SEED” is our recent paper that has just been accepted in Journal of Chemical Information and Modeling. In this paper we evaluate the performance of the fragment docking program SEED (Solvation Energy for Exhaustive Docking) on 15 different protein targets.
SEED has been evaluated with a focus on enrichment and hit rate. It is shown that SEED allows for consistent computational enrichment of fragment libraries, independent of the effective hit rate. Depending on the actual target protein, true positive rates ranging up to 27% are observed at a cutoff value corresponding to the experimental hit rate. The impact of variations in docking protocols and energy filters is discussed in detail. Remaining issues, limitations, and use cases of SEED are also discussed. Our results show that fragment library selection or enhancement for a particular target is likely to benefit from docking with SEED, suggesting that SEED is campaigns. A workflow is presented for the use of the program postprocessing to optimize hit rates.
Many thanks to Kenneth Goossens for the nice work!