firestar—advances in the prediction of functionally important residues
By Gonzalo López, P. Maietta, J. Rodríguez, Alfonso Valencia, Michael L. Tress. 2011
61 citations recorded by the source corpus.
firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Jianyi Yang
- Yang Zhang
- Ren Sun
- Alfonso Valencia
- Iakes Ezkurdia
- Michael L. Tress
- Tim J. P. Hubbard
- Robin Pearce
In Molecular Biology
- Yang Zhang
- Jianyi Yang
- Manolis Kellis
- Michael F. Lin
- Mark Diekhans
- Mark Gerstein
- S. Searle
- Rachel A. Harte
Citations in the corpus
- I-TASSER server: new development for protein structure and function predictions (2015, methodology): “We believe that the incorporation of other complementary ligand-binding site prediction methods, such as Firestar (13) and 3DLigandSite (14), would further improve the performance of the COACH method.”
- Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality (2015, methodology): “We tested three software approaches, firestar [69] and two classification schemes under FRpred [70, 71], namely FRcons and FRsubtype.”
- GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “(cid:129) firestar (Lopez et al. 2007, 2011) is a method that predicts functionally important residues in protein sequences.”
- FireDB: a compendium of biological and pharmacologically relevant ligands (2013, background): “FireDB has a companion web server, firestar (12,13) that bases its ligand binding and catalytic residue predictions on the binding sites in FireDB.”