SAND: a comprehensive annotation of class D β-lactamases using structural alignment-based numbering

Class D β-lactamases are a diverse group of enzymes that contribute to antibiotic resistance by inactivating β-lactam antibiotics. Examination of class D β-lactamases has evolved significantly over the years, with advancements in molecular biology and structural analysis providing deeper insights into their mechanisms of action and variation in specificity. However, one of the challenges in the field is the inconsistent residue numbering and secondary structure annotation across different studies, which complicates the comparison and interpretation of data. To address this, we propose SAND—a standardized naming system for both residues and secondary structure elements, based on a comprehensive structural alignment of all documented sequences and experimentally obtained crystal structures of class D β-lactamases. This unified framework will streamline cross-study comparisons and enhance data interpretation. Moreover, the standardized framework will enable AI-driven natural language processing (NLP) techniques to efficiently mine and compile relevant data from scientific literature, speeding up the discovery process and contributing to more rapid advancements in β-lactamase research.