Homology Groups

Homology groups stand for sets of homologous molecular parts (e.g. functional groups). These are represented by pseudo atoms labelled with the common chemical annotation of the groups (alkyl, aryl, heterocycle, etc.).

See the detailed definition of these groups in a separate document. The pseudo atoms can be most easily drawn in Marvin Sketch using the Homology Groups template group.

Example	Example Markush library member

There are two major types of homology groups regarding their way of definition:

1. Built-in homology groups are defined by specific structural properties of the group. These groups are not enumerated during the search, but appropriate substructures are recognized as fulfilling the requirements for such a structure. The possible number of covered structures is usually infinite, unless the number of atoms is limited. Examples of built-in groups are alkyl, aryl, heterocycle, etc.

2. User-defined homology groups are explicitly defined, and only the listed substructures can match on these homology groups. The definition is given in the form of an R-group definition, in which any generic Markush feature can be used. These definitions can be customized by the user, and may be context-specific. (E.g. protecting group definition depends on which functional group it protects.)

Read more about homology groups.