Name
Title | ||
|---|---|---|
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. |
Abstract | ||
|---|---|---|
Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at http://phosfinder.bio.uniroma2.it. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1093/nar/gkr389 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
internet,binding sites,protein conformation,proteins,nucleic | Protein family,Phosphate,Binding site,Biology,Ligand,Structural similarity,Bioinformatics,Computational biology,Genetics,Protein Data Bank (RCSB PDB),Web server,Protein structure | Journal |
Volume | Issue | ISSN |
39 | SUPnan | 0305-1048 |
Citations | PageRank | References |
3 | 0.43 | 15 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Luca Parca | 1 | 30 | 2.89 |
| Iolanda Mangone | 2 | 3 | 1.10 |
| Pier Federico Gherardini | 3 | 102 | 5.21 |
| Gabriele Ausiello | 4 | 301 | 23.59 |
| Manuela Helmer-Citterich | 5 | 456 | 33.41 |