The Dali server is a network service for comparing protein structures in 3D. It has been in operation for over 20 years and is widely used by crystallographers to analyze newly solved structures. The latest update enhances the server's ability to study sequence and structure conservation. The server offers three types of structure comparisons: (i) PDB search, which compares one query structure against those in the PDB and returns similar structures; (ii) pairwise comparison, which compares one query structure against a user-specified list of structures; and (iii) all-against-all comparison, which returns a structural similarity matrix, dendrogram, and multidimensional scaling projection of a set of user-specified structures. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. Combined structure-sequence alignment information is compressed into a stack of aligned sequence logos. Each structure is structurally aligned to the query protein and represented by a sequence logo. The Dali server has processed over 175,000 PDB searches in the last 8 years. The server's user interface has been updated, replacing Jmol with PV as the protein viewer. The primary output from a PDB search is an ordered list of structural neighbours. An option for all-against-all comparisons of a selected subset of structures has been added, visualizing structural relationships as a dendrogram. Correspondence analysis generates an alternative view of 'structure space'. Structural information can be leveraged to homologous proteins based on sequence comparison. The SANSparallel server is used to generate sequence profiles on the fly. Stacked sequence logos are introduced as a way to condense multiple sequence alignments. The Dali server performs three types of structure comparisons: PDB search, pairwise comparison, and all-against-all structure comparison. The all-against-all structure comparison is a new option that computes an N x N matrix of pairwise similarities. The server uses various heuristics to optimize the alignment score. The results are presented as plain text for downloading and as hypertext for interactive analysis. The server also provides a subset of matches to PDB90, filtered at 90% sequence identity. Selected subsets of matching structures can be visualized as stacked alignments, in 3D superimposition, or their amino acid sequences can be sent to other servers for further analysis. The Dali server provides tools to navigate, integrate, and organize data into a form that is easier to comprehend.The Dali server is a network service for comparing protein structures in 3D. It has been in operation for over 20 years and is widely used by crystallographers to analyze newly solved structures. The latest update enhances the server's ability to study sequence and structure conservation. The server offers three types of structure comparisons: (i) PDB search, which compares one query structure against those in the PDB and returns similar structures; (ii) pairwise comparison, which compares one query structure against a user-specified list of structures; and (iii) all-against-all comparison, which returns a structural similarity matrix, dendrogram, and multidimensional scaling projection of a set of user-specified structures. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. Combined structure-sequence alignment information is compressed into a stack of aligned sequence logos. Each structure is structurally aligned to the query protein and represented by a sequence logo. The Dali server has processed over 175,000 PDB searches in the last 8 years. The server's user interface has been updated, replacing Jmol with PV as the protein viewer. The primary output from a PDB search is an ordered list of structural neighbours. An option for all-against-all comparisons of a selected subset of structures has been added, visualizing structural relationships as a dendrogram. Correspondence analysis generates an alternative view of 'structure space'. Structural information can be leveraged to homologous proteins based on sequence comparison. The SANSparallel server is used to generate sequence profiles on the fly. Stacked sequence logos are introduced as a way to condense multiple sequence alignments. The Dali server performs three types of structure comparisons: PDB search, pairwise comparison, and all-against-all structure comparison. The all-against-all structure comparison is a new option that computes an N x N matrix of pairwise similarities. The server uses various heuristics to optimize the alignment score. The results are presented as plain text for downloading and as hypertext for interactive analysis. The server also provides a subset of matches to PDB90, filtered at 90% sequence identity. Selected subsets of matching structures can be visualized as stacked alignments, in 3D superimposition, or their amino acid sequences can be sent to other servers for further analysis. The Dali server provides tools to navigate, integrate, and organize data into a form that is easier to comprehend.