Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.06.23.546351v1?rss=1
Authors: Wei, H., Wang, W., Peng, Z., Yang, J.
Abstract:
Since its establishment in 2013, BioLiP has become one of the widely used databases for protein-ligand interactions. Nevertheless, several key issues occurred with it over the past decade. For example, the adopted format is single chains for both proteins and ligands, which is inappropriate as many interactions are formed with multiple protein chains (known as biological units) and multiple ligand chains (e.g., DNA). We sought to address these issues, resulting in BioLiP2, a new database for protein-ligand interactions. The major features of BioLiP2 include: (1) protein structures are in the form of biological units rather than single-chain 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 protein-ligand interactions are retained; (5) a new biological unit structure-based ligand-binding site prediction algorithm is developed. With these new features, BioLiP2 is expected to be a valuable resource for studying protein-ligand interactions. It is freely available at: http://yanglab.qd.sdu.edu.cn/BioLiP2/.
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