The Dali server, accessible at http://ekhidna.biocenter.helsinki.fi/dali_server, is a web-based platform for protein structure comparison. It consists of three main components: (i) the Dali server, which compares new structures against the Protein Data Bank (PDB), (ii) the Dali database, which allows browsing of precomputed structural neighborhoods, and (iii) the pairwise comparison tool, which generates suboptimal alignments for pairs of structures. The inputs can be PDB identifiers or user-uploaded structures, and the results are hyperlinked for interactive analysis. The server aims to identify conserved residues and ligands in multiple structural alignments, aiding in evolutionary discoveries. The Dali server processes up to eight PDB searches in parallel and returns results within a minute. The Dali database is updated twice a year and contains precomputed alignments of PDB90 against the full PDB. The pairwise comparison tool uses a systematic branch-and-bound search to return non-overlapping solutions. The server's effectiveness is evaluated using the SCOP classification, with an average AUC of 0.79, 0.87, and 0.92 at fold, superfamily, and family levels, respectively. An example of a putative bacterial cell invasion protein (PDB entry 3kk7) demonstrates the utility of the Dali server in identifying homologous proteins through interactive analysis.The Dali server, accessible at http://ekhidna.biocenter.helsinki.fi/dali_server, is a web-based platform for protein structure comparison. It consists of three main components: (i) the Dali server, which compares new structures against the Protein Data Bank (PDB), (ii) the Dali database, which allows browsing of precomputed structural neighborhoods, and (iii) the pairwise comparison tool, which generates suboptimal alignments for pairs of structures. The inputs can be PDB identifiers or user-uploaded structures, and the results are hyperlinked for interactive analysis. The server aims to identify conserved residues and ligands in multiple structural alignments, aiding in evolutionary discoveries. The Dali server processes up to eight PDB searches in parallel and returns results within a minute. The Dali database is updated twice a year and contains precomputed alignments of PDB90 against the full PDB. The pairwise comparison tool uses a systematic branch-and-bound search to return non-overlapping solutions. The server's effectiveness is evaluated using the SCOP classification, with an average AUC of 0.79, 0.87, and 0.92 at fold, superfamily, and family levels, respectively. An example of a putative bacterial cell invasion protein (PDB entry 3kk7) demonstrates the utility of the Dali server in identifying homologous proteins through interactive analysis.