title: 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.
abstract: 3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy. allegra.via@uniroma2.it
authors.forename: Allegra
authors.initials: A
authors.lastname: Via
authors.forename: Daniele
authors.initials: D
authors.lastname: Peluso
authors.forename: Pier Federico
authors.initials: PF
authors.lastname: Gherardini
authors.forename: Emanuele
authors.initials: E
authors.lastname: de Rinaldis
authors.forename: Teresa
authors.initials: T
authors.lastname: Colombo
authors.forename: Gabriele
authors.initials: G
authors.lastname: Ausiello
authors.forename: Manuela
authors.initials: M
authors.lastname: Helmer-Citterich
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D017124:Conserved Sequence; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D011381:Programming Languages; D011487:Protein Conformation; D016415:Sequence Alignment; D012984:Software; D040681:Structural Homology, Protein