FlexNovo for Linux (64-bit) is a new molecular design program based on the FlexX-technology of incrementally constructing a ligand in an active site. It facilitates a fragment-based approach to de novo design in the context of the 3D-structure of the target. It is meant to be an integrated and user-customizable idea-generating system. It suggests new structural motifs, designing libraries of lead-prototypes, and in proposing novel scaffolds as well as alternative binding modes for a target protein. It also facilitates the evolution of a ligand in the depth of the active site, if one starts. The software can be even more powerful if there is expert knowledge integrated, for example, considering key interactions with the target, specific chemical motifs, or certain physicochemical properties.