3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.
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/
Via
Allegra
A
Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy. allegra.via@uniroma2.it
Peluso
Daniele
D
Gherardini
Pier Federico
PF
de Rinaldis
Emanuele
E
Colombo
Teresa
T
Ausiello
Gabriele
G
Helmer-Citterich
Manuela
M
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