4.2.6 Build Files

Build files are generated as a convenience for further investigation of the fragments identified by Brood. Each build file contains the same fragments as in the corresponding hitlist, but the fragment has been placed in the context of the molecule specified by the -build parameter, replacing the query fragment. In other words, this file contains the whole molecules generated by replacing the query with each bioisosteric fragment in turn.

If the moleculed specified by the -build parameter doesn't contain 3D coordinates, then the analog molecules written to the build files will contain 2D depiction coordinates.

On the other hand, if the molecule specified by the -build parameter does contain 3D coordinates, the molecules written to the build files will also contain 3D coordinates. Further, the coordinates of the replaced fragment will be in the same position used for scoring. Additionally, the rest of the molecule will have 3D coordinates that are minimally perturbed from their position in the original molecule. Thus if the molecule specified by the -build parameter were a crystallographic ligand, the molecules written to the build files will be as close as possible to the location of the original molecule.

				Brood: Fragment replacement for Medicinal Chemistry

				Brood: Fragment replacement for Medicinal Chemistry