FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank.

ABSTRACT: This work presents Fragment Graph DataBase (FGDB), a graph database of ligand fragments extracted and generated from the protein entries available in the Protein Data Bank (PDB). FGDB is meant to support and elicit campaigns of fragment-based drug design, by enabling users to query it in order to construct ad hoc, target-specific libraries. In this regard, the database features more than 17 000 fragments, typically small, highly soluble and chemically stable molecules expressed via their canonical Simplified Molecular Input Line Entry System (SMILES) representation. For these fragments, the database provides information related to their contact frequencies with the amino acids, the ligands they are contained in and the proteins the latter bind to. The graph database can be queried via stan

SUBMITTER: Toti D 

PROVIDER: S-EPMC9239314 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature