Protein structure prediction on the Web: a case study using the Phyre server
By Lawrence A. Kelley, Michael J.E. Sternberg. Nature Protocols, 2009
4,562 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/97facaf1d4cc3647afb95c91e3984963ee153137
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
- Torsten Schwede
- Liam J. McGuffin
- Daniel B. Roche
- Lorenza Bordoli
- Andrej Sali
- Stuart J. Tetchner
- Yang Zhang
- David T. Jones
In Molecular Biology
- Liam J. McGuffin
- Torsten Schwede
- Yang Zhang
- David T. Jones
- Daniel B. Roche
- Andrej Sali
- Jinbo Xu
- Ben M. Webb
Citations in the corpus
- The Hcp proteins fused with diverse extended-toxin domains represent a novel pattern of antibacterial effectors in type VI secretion systems (2017, methodology): “The functional prediction was performed using HHpred52 and Phyre2.”
- A position-specific distance-dependent statistical potential for protein structure and functional study (2012, neutral): “These 18 servers are BAKER- ROSETTASERVER (Raman et al., 2009), chunk-TASSER (Zhou et al., 2009), chuo-fams (Kanou et al., 2009), CLEF-Server (Shao et al., 2011), FAMSD (Kanou et al., 2009), gws (Joo et al., 2009), HHpredA (Hildebrand et al., 2009), Jiang_Assembly (Hu et al., 2011), MULTICOM-CLUSTER”
- Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “Since then, many more services have been developed to model the structures of proteins in an automated manner (21, 22), e.g. ModWeb (23), Robetta (24), HHpred (25), I-TASSER (26), Pcons (27), PHYRE (28), or M4T (29).”
- Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, neutral): “…(Pieper et al., 2011; Yang et al., 2012) Pcons.net http://pcons.net/ (Larsson et al., 2011) PHYRE2 http://www.sbg.bio.ic.ac.uk/phyre2/ (Kelley and Sternberg, 2009) Robetta http://robetta.bakerlab.org/ (Raman et al., 2009) Rosetta https://www.rosettacommons.org (Das and Baker,…”
- The Glycosyltransferase Repertoire of the Spikemoss Selaginella moellendorffii and a Comparative Study of Its Cell Wall (2012, positive): “CDD does not cover all families, for those families not covered, fold prediction by the Phyre-server was employed [110].”
- Genome3D: exploiting structure to help users understand their sequences (2014, background): “PHYRE2 (6) Sternberg/Kelley Imperial Prediction: Both SCOP/PDB SUPERFAMILY (7) Gough Bristol Prediction: Both SCOP VIVACE Blundell Cambridge Prediction: Models CATH/SCOP CATH (8) Orengo UCL Classification N/A”
- Computational Methods in Drug Discovery (2014, methodology): “are available if PDB-BLAST does not yield any hits (Kelley and Sternberg, 2009; Soding and Remmert, 2011).”
- A highly conserved program of neuronal microexons is misregulated in autistic brains (2014, methodology): “Next, we modeled the structure of microexon-containing Ensembl proteins using the Phyre fold-recognition server (Kelley and Sternberg, 2009), with default parameters.”