Defining and Selecting Fragments

Why build molecules from fragments? We suppose that it is reasonable to use molecular sub-units which have "functional group" status in the domain of interest (e.g., medicinal chemistry). If this is correct, the remaining problem is to identify these fragments.

The definition of a fragment for GADD is inspired by the definition of ClogP fragments.

ClogP fragments are defined by isolating carbons, carbons not double or triple bonded to hetero atoms. When ICs are removed, what's left are ClogP fragments.

For GADD, we also define "carbon fragments" as what's left after ClogP fragments are removed.

Example:

Benzylpenicillin
FRAGs in blue,
CFRAGs in yellow

Four FRAGs:

Three CFRAGs:

Note from this definition that fragments always attach to carbon fragments and vice versa. Inter-fragment bonds are always between ICs and non-ICs.

Attachment points are distinguished by the bond order. In ClogP, the type of attached atom is also part of the fragment definition (the environment). In GADD we ignore this -- for now.

However, GADD is not tied to any fragment selection strategy. Any approach from single atoms on up is possible.

Fragments may be extracted from existing databases of molecules. A separate program cpfrags.c has been written for this purpose.

MUG'01 -- 6-9 March 2001 -- Santa Fe, NM

Daylight Chemical Information Systems Inc.
info@daylight.com

Benzylpenicillin FRAGs in blue, CFRAGs in yellow
Four FRAGs:
Three CFRAGs: