Kernel Energy Method (KEM)
KEM was introduced by Huang et al.34. The original study looks at peptides and chooses each fragment to be one amino acid. The severed bonds are then capped with Simple Replacement capping scheme (this conclusion is based on the fact that the manuscript states that hydrogen atoms are added to cap the severed bonds, but provides no additional details). The manuscript starts by testing a screening method where only chemically bonded dimers are considered. Compared to supersystem energies, this screening method results in larger errors (10s to 100s of kcal/mol). Using larger fragments reduces the error (how the larger fragments were formed is not clear), as does considering all dimers.
Name |
Fragments |
Embedding |
Caps |
Screening |
|---|---|---|---|---|
KEM |
N/A |
N/A |
N/A |