We report comprehensive fragment libraries obtained from large natural product databases and compare their chemical space coverage and diversity with those of synthetic fragment libraries. Specifically, we obtained 2,583,127 fragments derived from the recently updated collection of open natural product (COCONUT) data set with more than 695,133 unique (nonduplicate) natural products and 74,193 fragments derived from the Latin America Natural Product Database (LANaPDB) with 13,578 unique natural products from Latin America. The content, chemical space coverage, and chemical diversity of the natural product libraries were compared to the recently developed CRAFT library, which contains 1214 fragments based on distinct heterocyclic scaffolds and natural product-derived chemicals. The fragment libraries herein obtained and curated are freely available at https://github.com/DIFACQUIM/Fragment-libraries-from-large-synthetic-compounds-and-natural-products-collections.git.
© 2025 The Authors. Published by American Chemical Society.