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3dLOGO: a web server for the identification, analysis and use of conserved protein substructures

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Item Type:Article
Title:3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
Creators Name:Via, A. and Peluso, D. and Gherardini, P.F. and Rinaldis, E.D. and Colombo, T. and Ausiello, G. and Helmer-Citterich, M.
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/
Keywords:Algorithms, Amino Acid Sequence, Computational Biology, Computer Graphics, Conserved Sequence, Protein Databases, Internet, Molecular Models, Programming Languages, Protein Conformation, Sequence Alignment, Software, Protein Structural Homology
Source:Nucleic Acids Research
Publisher:Oxford University Press
Number:Web Server Issue
Page Range:W416-W419
Date:July 2007
Official Publication:https://doi.org/10.1093/nar/gkm228
PubMed:View item in PubMed

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