Since its establishment in 2013, BioLiP has become one of the widely used resources for protein-ligand interactions. Nevertheless, several known issues occurred with it over the past decade. For example, the protein-ligand interactions are represented in the form of single-chain-based tertiary structures, which may be inappropriate as many interactions involve multiple protein chains (known as quaternary structures). We sought to address these issues, resulting in Q-BioLiP, a comprehensive resource for quaternary structure-based protein-ligand interactions. The major features of Q-BioLiP include: (1) protein structures are represented in the form of quaternary structures rather than single-chain-based tertiary structures; (2) DNA/RNA chains are properly paired rather than separated; (3) both experimental and predicted binding affinities are provided; (4) both biologically relevant and irrelevant interactions are retained to alleviate the problem of the wrong justification of ligands' biological relevance; (5) a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure is developed. With these new features, Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions, including protein-small molecule, protein-peptide, protein-protein, and protein-DNA/RNA. Q-BioLiP is freely available at: https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.Competing Interest StatementThe authors have declared no competing interest.Footnotes* The name of the database has been updated to Q-BioLiP....

Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions

10.1101/2023.06.23.546351