FragmentStore - a comprehensive database of fragments linking metabolites, toxic molecules and drugs

Consideration of biomolecules in terms of their molecular building blocks provides valuable new information regarding their synthesis, degradation and similarity. Here, we present the FragmentStore, a resource for the comparison of fragments found in metabolites, drugs or toxic compounds. Starting from 13 000 metabolites, 16 000 drugs and 2200 toxic compounds we generated 35 000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding sideeffects and toxicity. The FragmentStore provides a variety of search options such as 2D structure, molecular weight, rotatable bonds, etc. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments’ binding sites, classification of fragments based on the enzyme classification class of the enzyme(s) they bind to and small molecule library generation via a fragment-assembler tool. Using the FragmentStore,...

• Type: Journal
• Year: 2011
• Where: NAR
• Authors: Jessica Ahmed, Catherine L. Worth, Paul Florian Thaben, Christian Matzig, Corinna Blasse, Mathias Dunkel, Robert Preissner
• Keywords: Enzyme Classification, Molecule Library, NAR 2011, Toxic Compounds