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bioRxiv · 10.1101/2023.06.23.546351

BioLiP2: a database for biological unit-based protein-ligand interactions

Wei, H.·Wang, W.·Peng, Z.·Yang, J.
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Abstract

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) representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures; (2) pairing DNA/RNA chains properly rather than separation; (3) providing both experimental and predicted binding affinities; (4) retaining both biologically relevant and irrelevant interactions to alleviate the problem of the wrong justification of ligands biological relevance; and (5) developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure. 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/.

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Wei, H., Wang, W., Peng, Z., Yang, J.. 2023-06-26. BioLiP2: a database for biological unit-based protein-ligand interactions. https://doi.org/10.1101/2023.06.23.546351

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