Paper Info
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/.
Year
DOI
Venue
2007
10.1093/nar/gkm228
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
protein conformation,computer graphics,protein structure,computational biology,structure alignment,algorithms,protein data bank,internet,sequence alignment,conserved sequence,amino acid sequence,programming languages
Sequence alignment,Sequence logo,Conserved sequence,Structural alignment,Biology,Theoretical computer science,Bioinformatics,Protein Data Bank,Genetics,Protein Data Bank (RCSB PDB),Web server,Protein structure
Journal
Volume
Issue
ISSN
35
SUPnan
0305-1048
Citations 
PageRank 
References 
2
0.39
11
Authors
7
Name
Order
Citations
PageRank
Allegra Via161644.62
Daniele Peluso247522.09
Pier Federico Gherardini31025.21
Emanuele de Rinaldis4291.10
Teresa Colombo5181.92
Gabriele Ausiello630123.59
Manuela Helmer-Citterich745633.41