# AlphaFold3

This work presents AlphaBridge, a reproducible, objective, and automated toolkit, also available as a web server, that combines AlphaFold3 confidence metrics to cluster sequence motifs participating in binary interactions and subsequently in 3D interfaces of complexes, visualizes interaction interfaces within confidence limits via chord diagrams, network graphs, and summary tables of predicted interfaces and intermolecular interactions linked to interactive graphics, and was validated for scoring binary and multi-component protein complexes with real-life examples discussed.

This work presents AlphaBridge, a reproducible, objective, and automated toolkit, also available as a web server, that combines AlphaFold3 confidence metrics to cluster sequence motifs participating in binary interactions and subsequently in 3D interfaces of complexes, visualizes interaction interfaces within confidence limits via chord diagrams, network graphs, and summary tables of predicted interfaces and intermolecular interactions linked to interactive graphics, and was validated for scoring binary and multi-component protein complexes with real-life examples discussed.

This study devised a bioinformatics pipeline for a comparative analysis of mechanosensitive membrane proteins in lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus) and a fungus (Pleurotus floridanus), generating a consensus sequence for P. floridanus via multiple sequence alignment of homologues and mapping it onto the genome with BLAST to delineate the gene region of interest, then producing protein structures with the AlphaFold3 artificial intelligence platform using the correct oligomeric state for each channel, thereby bridging the structural knowledge gap for mechanoreceptors in these non-model systems.

This study devised a bioinformatics pipeline for a comparative analysis of mechanosensitive membrane proteins in lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus) and a fungus (Pleurotus floridanus), generating a consensus sequence for P. floridanus via multiple sequence alignment of homologues and mapping it onto the genome with BLAST to delineate the gene region of interest, then producing protein structures with the AlphaFold3 artificial intelligence platform using the correct oligomeric state for each channel, thereby bridging the structural knowledge gap for mechanoreceptors in these non-model systems.