Drug-Like, Shape Profiling and Diversity Assessment of the Molport in-Stock Compound Database

Abstract

Publicly accessible compound repositories are essential for virtual screening and hit identification, but their continuous growth brings inconsistent structure representations, reactive groups, and a computational burden from standardizing millions of entries. Many repositories also contain outdated or out-of-stock compounds that are no longer procurable, weakening the practical value of screening results. We present a 20-year effort to build and maintain an open-access compound repository: the Molport in-stock catalog, now a collection of 6.1 M purchasable compounds sourced exclusively from validated suppliers. We describe the cheminformatics workflow applied to this catalog, which harmonizes structures from openly accessible, heterogeneous sources into a standardized format, maintains dynamic currency by including only compounds confirmed in stock and removing outdated or unavailable molecules, and profiles physicochemical properties, druglikeness, three-dimensional (3D) shape, and structural diversity to produce chemically meaningful, medicinally relevant subsets. The result is an organized, up-to-date view of purchasable chemical space that supports faster and more reliable identification of experimentally accessible hit candidates for downstream screening campaigns.