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, A., Peluso, D., Gherardini, P., de Rinaldis, E., Colombo, T., Ausiello, G., et al. (2007). 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. NUCLEIC ACIDS RESEARCH, 35(Web Server issue), W416-W419 [10.1093/nar/gkm228].

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

Gherardini, PF;AUSIELLO, GABRIELE;HELMER CITTERICH, MANUELA
2007-07-01

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/
1-lug-2007
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore BIO/11
English
Con Impact Factor ISI
Computational Biology; Conserved Sequence; Protein Conformation; Structural Homology, Protein; Internet; Programming Languages; Models, Molecular; Computer Graphics; Software; Databases, Protein; Sequence Alignment; Amino Acid Sequence; Algorithms
http://nar.oxfordjournals.org/content/35/suppl_2/W416.long
Via, A., Peluso, D., Gherardini, P., de Rinaldis, E., Colombo, T., Ausiello, G., et al. (2007). 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. NUCLEIC ACIDS RESEARCH, 35(Web Server issue), W416-W419 [10.1093/nar/gkm228].
Via, A; Peluso, D; Gherardini, P; de Rinaldis, E; Colombo, T; Ausiello, G; HELMER CITTERICH, M
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/15194
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