title: Dali server update.
abstract: The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo.
authors.affiliation: Institute of Biotechnology, University of Helsinki, PO Box 56, Finland Department of Biosciences, University of Helsinki, PO Box 56, Finland Liisa.Holm@helsinki.fi.
authors.forename: Liisa
authors.initials: L
authors.lastname: Holm
authors.affiliation: Institute of Biotechnology, University of Helsinki, PO Box 56, Finland.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Laakso
mesh_terms: D000465:Algorithms; D000581:Amidohydrolases / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D000595:Amino Acid Sequence; D003196:Computer Graphics; D030541:Databases, Genetic; D006801:Humans; D021621:Imaging, Three-Dimensional; D020407:Internet; D008958:Models, Molecular; D010802:Phylogeny; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D040681:Structural Homology, Protein; D014584:User-Computer Interface
chemical_list: D000581:Amidohydrolases