Biochemical and Organic Model Builder — a molecule-building program that grows candidate compounds atom by atom inside a protein binding site, then scores and ranks what it has made.
Most virtual screening starts from a catalogue: you take compounds that already exist and ask which of them might fit. BOMB works the other way round. Given a protein structure, it constructs candidate molecules directly in the binding site — choosing a core, then growing substituents onto it position by position, combinatorially — and scores the results where they sit.
That makes it a design program rather than a search program. The libraries it enumerates need not exist anywhere; the point is to find what should be made.
BOMB is not a front end to anything and is not built on the Monte Carlo codes. It is its own molecule-building program — but what it proposes has an obvious next step, and that is where the rest of the toolkit picks up.
Builds and ranks candidate molecules inside the binding site, turning a target structure into a shortlist of compounds worth considering.
The shortlisted analogs can then be taken through rigorous free-energy perturbation to get relative binding affinities before anything is synthesized.
MCPRO →There is no separate BOMB methods paper — the program is described within the lead-discovery work above.