Boston De Novo Design
Regine Bohacek, PhD
 
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Evaluation by AlleGrow

In current versions of AlleGrow, each building block is evaluated according to the number of hydrophobic interactions and the number of hydrogen bonds that the new atoms form with binding site atoms.

Cutoff distances between binding site atoms and newly generated AlleGrow atoms can be specified by the user.

The minimum and maximum distance defining a hydrogen bond can also be set be specified.

Future plans: Incorporation of the improved scoring functions used by the AlleGrow heterocycle or side chain growing modules .

Evaluation using AlleGrow's heterocycle or side chain modules

Atoms generated by AlleGrow using the heterocycle or side chain libraries are evaluated using a simple potential function with terms for contact energy, hydrogen bonding energy, polar desolvation and complementarily "mismatch".

Coefficients for the weight of each of these terms can be adjusted by the user to bias the type of interactions desired.