Phyre protocols

Phyre specifications


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


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  • person_outline Michael Sternberg <>
  • person_outline Lawrence Kelley <>

Publications for Protein Homology/analogy Recognition Engine

Phyre IN pipelines

PMCID: 5788867
PMID: 29379064
DOI: 10.1038/s41598-018-20137-2

[…] 1g10 monoclonal antibody (fig. 1d). this indicated that the trypsin action did not affect the exposure of the neutralizing epitopes., the 3d structure models of all the proteins were predicted using phyre2 protein fold recognition server. after refinement and quality assessment, only the best ranked models were selected for further analysis. the protein–protein docking was performed using […]

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 (32)., for crf-bp, top scoring models produced by threading-based approaches identified by muster and phyre2 servers (33, 34) were retrieved, aligned, and used as starting templates to generate a human crf-bp model. fragments from gastric intrinsic factor receptor cubilin (pdb: 3kq4) (35) […]

PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] hhpred were of low sequence identity and in order to gain confidence on the fold assignment, further the same region of gcn1 was analysed using other fold recognition methods such as lomets [17] and phyre2 [18]. all the independent hmm matching and fold recognition methods employed consistently predicted heat repeat containing proteins as related to the 2159–2641 region of gcn1 (additional file […]

PMCID: 5487728
PMID: 28655817
DOI: 10.1128/mBio.00078-17

[…] data bank ( (42). a sequence alignment of human neu3 and neu2 was performed with clustal w (43). a model of neu3 was then made with the software programs swiss-model (44) and phyre (45) on the basis of the crystal structures of neu2 (pdb codes 1so7 [sugar-induced form], 1vcu [inhibitor dana form], and 1snt [apo form]) (46). the pymol program (47) was used for model […]

PMCID: 5524358
PMID: 28742131
DOI: 10.1371/journal.pone.0181940

[…] was used to search for protein domains. protein disulfide bonds were predicted using dipro (, molecular modeling of mature ataga and lhaga was done with the phyre server using default parameters ( [25]. for both proteins, the model with highest confidence (100%) and coverage (76% and 75% for ataga and lhaga, […]

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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