PDBe tools for an in‐depth analysis of small molecules in the Protein Data Bank

Citations Over TimeTop 10% of 2025 papers

Abstract

The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small molecules bound to the macromolecules. Despite the extensive data available, the complexity of small-molecule data in the PDB necessitates specialized tools for effective analysis and visualization. PDBe has developed a number of tools, including PDBe CCDUtils (https://github.com/PDBeurope/ccdutils) for accessing and enriching ligand data, PDBe Arpeggio (https://github.com/PDBeurope/arpeggio) for analyzing interactions between ligands and macromolecules, and PDBe RelLig (https://github.com/PDBeurope/rellig) for identifying the functional roles of ligands (such as reactants, cofactors, or drug-like molecules) within protein-ligand complexes. The enhanced ligand annotations and data generated by these tools are presented on the novel PDBe-KB ligand pages, offering a comprehensive overview of small molecules and providing valuable insights into their biological contexts (example page for Imatinib: https://pdbe.org/chem/sti). By improving the standardization of ligand identification, adding various annotations, and offering advanced visualization capabilities, these tools help researchers navigate the complexities of small molecules and their roles in biological systems, facilitating mechanistic understanding of biological functions. The ongoing enhancements to these resources are designed to support the scientific community in gaining valuable insights into ligands and their applications across various fields, including drug discovery, molecular biology, systems biology, structural biology, and pharmacology.

Related Papers

• → RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences(2020)1,531 cited
• → RCSB Protein Data Bank: Enabling biomedical research and drug discovery(2019)349 cited
• → RCSB Protein Data Bank: A Resource for Chemical, Biochemical, and Structural Explorations of Large and Small Biomolecules(2016)146 cited
• → RCSB Protein Data Bank: celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D(2021)18 cited
• → The Research Collaboratory for Structural Bioinformatics Protein Data Bank(2007)24 cited