Phyre protocols

View Phyre computational protocol

Phyre statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Secondary structure prediction Tertiary structure prediction Structure visualization Amino acid sequence homology search Structural domain prediction Structure homology search chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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 in pipelines

 (201)
2018
PMCID: 5826306
PMID: 29515519
DOI: 10.3389/fendo.2018.00043

[…] 1go9) containing a d-phe residue at position 12 and alpha-aminoisobutyric acid in position 15 ()., for crf-bp, top scoring models produced by threading-based approaches identified by muster and phyre2 servers (, ) were retrieved, aligned, and used as starting templates to generate a human crf-bp model. fragments from gastric intrinsic factor receptor cubilin (pdb: 3kq4) () and neuropilin […]

2018
PMCID: 5838018
PMID: 29546036
DOI: 10.3389/fcimb.2018.00053

[…] by the ncbi blast service program. sequence alignments were generated using the clustalw2 program (blackshields et al., )., ehvps2, ehvps20, and ehvps24 amino acid sequences were submitted to the phyre2 server (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) to obtain the proteins 3d predicted structures. results obtained were documented and analyzed through the ucsf chimera […]

2018
PMCID: 5863359
PMID: 29588659
DOI: 10.1186/s13068-018-1074-3

[…] the corresponding pul. based on these criteria, fjoacxe (puldb id: fjoh_3879; genbank id: abq06890.1) was selected for recombinant protein expression. a structural model of fjoacxe was built using phyre2.0 [] for the cbm-like domain, using pdb 2o14 as template, and modeller 9.19 [] for the ce/catalytic domain using pdb 2o14 and pdb 1k7c []. the model was displayed with pymolv1.7.4.5 edu (pymol […]

2018
PMCID: 5876318
PMID: 29628932
DOI: 10.3389/fpls.2018.00334

[…] we analyzed the protein structure of the region comprising the end of the i domain through the c domain of the three thalictrum ap3 proteins using protein homology/analogy recognition engine v 2.0 (phyre2; )., to investigate the function of three b-class gene orthologs of the ranunculid t. thalictroides, we conducted targeted vigs using single gene constructs, analyzed gene expression […]

2018
PMCID: 5883049
PMID: 29615685
DOI: 10.1038/s41598-018-23761-0

[…] the exon/intron structures of the cadirs were searched and presented as described by kang et al.. prediction of the tertiary structures and homologs of cadirs was conducted through the online server phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id = index) as described by li et al.., information about the chromosomal location of cadirs was obtained from the pepper genome platform […]


To access a full list of citations, you will need to upgrade to our premium service.

Phyre in publications

 (1593)
PMCID: 5964351
DOI: 10.1128/mBio.00869-18

[…] structurally compare to known human and animal norovirus capsids, we utilized predictive structural modeling to illustrate the full-length btcalv/a10 and btnov capsid structures. first, we used phyre2 open source software to determine if btcalv/a10 contained known calicivirus capsid structures followed by structural homology modeling using modeller software from the max planck institute […]

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

[…] well-conserved region (exon 4 to exon 5) within the ocia domain (fig. ). interestingly, in silico analysis using various structure prediction programs such as raptorx (raptorx.uchicago.edu/) and phyre (http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index) showed that the region ranging from exon 3 to exon 6 is indeed an important part of the ociad1/2 genes as it codes for a double […]

PMCID: 5955458
PMID: 29726306
DOI: 10.1080/21505594.2018.1451284

[…] with migaslllgav (www.giardiadb.org). cp14019 shows 80% identity to cp16779 and 50% identity to cp10217 and cp16160. the structures of the pro- and mature proteases were predicted using itasser and phyre2 and the structural models aligned well with known cathepsin b structures (fig. s1 to s3, table s3 to s5). cp10217, cp14019 and cp16779 are most similar to trypanosoma congolese procathepsin […]

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

[…] of 6.6 å (fsc = 0.5)., 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. […]

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

[…] (, fig. ). a topological model of the ipo13 polypeptide was predicted using smart (http://smart.embl-heidelberg.de/). the crystal structures of wild-type and mutant proteins were predicted using phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and visualized with the pymol software (version 1.5)., total rna was extracted from murine (c57bl/6 strain) tissues, including […]


To access a full list of publications, you will need to upgrade to our premium service.

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).

Phyre reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Phyre