New Paper: SiteMine: Large-scale binding site similarity searching in protein structure databases

30 May 2024

Photo: Thorben Reim

Drug discovery and design pose various challenges such as drug repurposing, analysis of protein-ligand and protein-protein complexes, ligand promiscuity studies, and function prediction. These challenges can be addressed through protein binding site similarity analysis.

Our newly introduced software tool, SiteMine, provides a comprehensive, database-driven, and alignment-providing binding site similarity search. SiteMine effectively tackles the most critical challenges in binding site comparison, offering a reliable, all-in-one solution. Extensive benchmarking on the ProSPECCTs dataset demonstrates SiteMine's promising performance across various criteria, ensuring dependable binding site comparisons. This paper outlines the functionality of SiteMine and its fundamental concepts. A specific application scenario highlights the structural similarities and dissimilarities between cathepsin L and calpain 1 binding sites, demonstrating the potential impact of these findings on structure-based drug design.

SiteMine can be downloaded from our NAOMI ChemBio software collection at https://uhh.de/naomi.