bindingssite

BindingsSite is a collaborative online resource that catalogs binding sites in biomolecules, including proteins, nucleic acids, and small-molecule ligands. The database integrates structural data with annotations describing pocket geometry, residue composition, physicochemical properties, and evidence for binding, whether experimental or computational. It aims to standardize terminology and provide machine-readable records to support research in structural biology, medicinal chemistry, and enzyme mechanism studies.

Origins and scope: BindingsSite was initiated by a consortium of structural biologists and bioinformaticians in response to fragmentation among published binding-site data. It covers experimentally characterized binding pockets as well as predicted sites, and it links each binding site to the corresponding macromolecule structure and, when available, ligand information and binding affinities or assays.

Data model and access: Each entry includes the host molecule identifier, binding-site residues, pocket coordinates, and optional annotations such as conservation scores, drug-likeness of ligands, and confidence levels. The platform provides search and filtering by pocket size, residue makeup, or geometry, and offers bulk downloads and an API for programmatic access. Submissions are community-driven and subject to editorial review to maintain quality.

Impact and limitations: BindingsSite is used in structure-based drug design, functional annotation of proteins, and education. Limitations include variable annotation depth across entries, incomplete coverage of novel structures, and reliance on the quality of source data. The project emphasizes ongoing curation and collaboration with existing databases such as sc-PDB, BioLiP, and Binding MOAD.

See also: sc-PDB, BioLiP, Binding MOAD.