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Protocols

Phyre specifications

Information


Unique identifier OMICS_06087
Name Phyre
Alternative names Protein Homology/analogy Recognition Engine, 3DPSSM, Phyre2, 3D-PSSM
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data An amino acid sequence.
Input format FASTA,RAW
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Subtools


  • BackPhyre
  • Phyre Investigator
  • PhyreAlarm

Documentation


Maintainers


  • person_outline Michael Sternberg
  • person_outline Lawrence Kelley

Publications for Protein Homology/analogy Recognition Engine

Phyre citations

 (1281)
call_split

Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

2018
MBio
PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] The full-length BtCalV/A10, GII.4.1997.Lordsdale HuNoV, GI.1 human sapovirus, GV.1 MNV, and BtNoV capsid sequences () were submitted to the Protein Homology/analogy Recognition Engine V2.0 (PHYRE2) server () and analyzed using Intensive Mode. Homology modeling of the BtCalV/A10 and BtNoV sequences was based on the known HuNoV GII.4/VA387 (PDB ID: 2OBT) () and HuNoV GII.4.2012/NSW0514 bou […]

library_books

A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation

2018
Sci Rep
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] vels of ociad1 and ociad2. For predicting structure of zebrafish, mouse, and human OCIAD1 and OCIAD2 proteins, various structure prediction programs such as RaptorX (http://raptorx.uchicago.edu/) and Phyre (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) were used wherein the amino acid sequences of these proteins corresponding to Uniprot IDs Q6NYD7, Q9CRD0, Q9NX40, Q5RHX2, Q9D8W7 and Q […]

library_books

Structure and mechanism of the two component α helical pore forming toxin YaxAB

2018
Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] Given the good quality of our cryo-EM map, unambiguous assignment of YaxA and YaxB was straightforward (see Supplementary Movie ). A full model of YaxB was obtained with the Phyre2 One-to-one threading service based on the complete model of PaxB (chain A). YaxA and YaxB were first placed by rigid body fitting of the monomers into the density map using Coot. Further implem […]

library_books

Mutation of IPO13 causes recessive ocular coloboma, microphthalmia, and cataract

2018
PMCID: 5938035
PMID: 29700284
DOI: 10.1038/s12276-018-0079-0

[…] analyses. Multiple orthologous sequence alignment revealed that R111C has been identified in a highly conserved region across different species (Fig. ). We then performed molecular modeling with the Phyre2 server in automated mode. The variant R111C was found to be located in the helix domain, which could serve to increase the number of hydrogen bonds within the surrounding space (Fig. ). These f […]

library_books

Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 β 1,4 xylosidase from Geobacillus thermoleovorans IT 08

2018
PLoS One
PMCID: 5919610
PMID: 29698436
DOI: 10.1371/journal.pone.0196358

[…] function [].Besides its presence in GH43 enzymes, β-sandwich domains are also present in β-glucanases, lectins, cellulases, laminarinases, and sialidases, as revealed by a search with the DALI [] and PHYRE [] servers. The highest structural similarity to a non-GH43 enzyme is observed for the hybrid Bacillus (1,3–1,4)-β-glucanase H(A16-M) (PDB 1AYH; DALI Z-score 14.8; RMSD of 3.0 Å for 164 Cα atoms […]

library_books

Two P1B 1 ATPases of Amanita strobiliformis With Distinct Properties in Cu/Ag Transport

2018
Front Microbiol
PMCID: 5924815
PMID: 29740406
DOI: 10.3389/fmicb.2018.00747

[…] ions in silico at the CCTOP web server (). The signal peptide prediction was also done by submitting the sequences to SignalP 4.1 server (). The homology modeling of transporter 3D structure used the Phyre2 protein homology/analogy recognition engine (), the Modeller (), and UCSF Chimera () programs. The closest AsCRD1 and AsCCC2 homologs among the RCSB Protein Data Bank (PDB) entries used for com […]

Citations

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Phyre institution(s)
Structural Bioinformatics Group, Imperial College London, London, UK
Phyre funding source(s)
Supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/J019240/1, BB/F020481/1), the Medical Research Council (MRC) (MRC Standard Research Student (DTA) G1000390-1/1) and the Engineering and Physical Sciences Research Council (EPSRC) (EPSRC Standard Research Student (DTG) EP/K502856/1).

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