Counting strands in outer membrane β-barrels

β-Barrel structures are critical components of bacterial outer membranes, where they facilitate transport, cell signaling, antibiotic resistance, and structural integrity. A key feature of β-barrels is their strand count, which influences pore diameter, binding site locations, and functional properties. However, because of breaks in strands and the presence of strands in periplasmic domains and plug domains, manual counting is inefficient and current algorithms do not accurately determine barrel strand count. To address this, we refined our previous β-barrel structural assessment tool, PolarBearal, to improve strand number identification in large-scale data sets. To enhance the accuracy of barrel strand number labeling, our updated algorithm integrates three structural criteria, namely inter-residue vector angles, hydrogen-bonding distances, and strand connectivity. Using this algorithm, we labeled strand numbers for 571,659 predicted outer membrane β-barrel structures obtained from the AlphaFold2 database. Our algorithm has 97% accuracy in strand number assignments, and the resulting data set facilitates assessment of the homogeneity of strand counts for different types of outer membrane proteins. The strand labeling also provides insights on β-barrel strand distribution and evolutionary patterns, supporting further research in protein structure prediction and design.