Phyre pipeline

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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  • Phyre Investigator



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

Publications for Protein Homology/analogy Recognition Engine

Phyre citations

PMCID: 5788867

[…] 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: 5623714

[…] and 1.2 å resolution structure of msmeg_3380 [pdb: 3f7e (taylor et al., 2010)]. the structure of the 26 residues missing from the msmeg_2027 crystal structure was predicted by homology modeling in phyre2 (intensive mode) (kelley et al., 2015) using m. tuberculosis rv3547/ddn [pdb: 3rz (cellitti et al., 2012)] as the template. simulations were visualized in the vmd: visual molecular dynamics […]

PMCID: 5161316

[…] model) (score 265.83; e-value: 2.9e-42; identity: 35%). the best templates for the tcrpa-1 and tcrpa-2 models were chosen according to data obtained from the profile-based threading method program phyre2 [22]. subsequently, these initial models were subjected to molecular dynamics (md) simulations executed by gromacs (groningen machine for chemical simulation) v.4.5.3 [23] in the presence […]

PMCID: 4852461

[…] helix lengths. previous published analysis suggests that this region of human separase is composed of arm or heat repeats [25,26]. fold recognition predictions carried out using hhpred [34] and phyre2 [35] matched the n-terminal regions of separase from h. sapiens, s. cerevisiae and c. elegans to helical and super-helical structures such as tpr repeats, and, with less confidence, arm […]

PMCID: 4631893

[…] not only the low percentage of identity between pappx and aappx [27] but also the homology in secondary structure, the model was constructed by threading using the “one-to-one threading” option of phyre server [27] ( the model was obtained with 100% of confidence and 292 residues of a total of 314 were aligned. tautomeric states of histidine residues […]

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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