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Expert Mode

One-to-one threading

Submit both a sequence and a structure. Phyre will attempt to align the sequence and structure and construct a model of your sequence

One to one threading
E-mail address
Optional job description
Amino Acid Sequence
or upload contents of sequence file
or UniProt accession
Upload PDB format file	Single chain only
or AlphaFold Model	"best" model or UniProt ID confidence

Batch processing

Submit a file containing up to 100 sequences for automated modelling by Phyre (to increase limit contact Harry Powell)

Batch processing
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Job description
Upload file of FASTA sequences (Max 100 seqs)		Phyre3-β

MSA options
E-mail address
Optional job description
Multiple sequence alignment
Or upload alignment
Alignment format	FASTA CLUSTAL Stockholm A2M A3M EMBL MEGA GCG/MSF PIR/NBRF TREECON
Alignment method	local global
Secondary structure scoring	yes no predicted vs predicted only
Secondary structure weight	0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9

BackPhyre

Use Phyre in reverse. Submit a PDB structure and search that structure against a wide range of genomes

Backphyre options
E-mail address
Optional job description
Upload PDB format file	Single chain only
Choose 1 or more genomes to search (ctrl-click or cmd-click) * private genomes (only searchable by associated users)	Agrobacterium_tumefaciens_C58_Cereon Aplysia_californica Arabidopsis_thaliana Archaeon_GW2011_AR3 Archaeon_GW2011_AR5 Archaeon_GW2011_AR17 Autotransporters Bacillus_subtilis Bartonella_henselae_Houston-1 Bdellovibrio_bacteriovorus Bodo_saltans Caenorhabditis_elegans_WS244 Caenorhabditis_elegans.WS220.66 Caulobacter_crescents Clostridium_difficile Corynebacterium_diphtheriae Desulfitobacterium_hafniense_Y51 Drosophila_melanogaster Enterobacteria_phage_T4 Escherichia_coli_K12 Francisella_novicida_U112 * GiardiaDB-37 Homo_sapiens Lactobacillus_casei_ATCC_334 Leishmania_major Listeria_monocytogenes Mus_musculus Mycobacterium_tuberculosis_CDC1551 Nanoarchaeota_archaeon_SCGC_AAA011-K22 Nanoarchaeota_archaeon_SCGC_AAA011-L22 Nanoarchaeota_SCGC_G17_aa Nanoarchaeote_nst1_aa Nanoarchaeum_equitans_aa Neisseria_meningitidis_MC58 Plasmodium_falciparum Pseudomonas_aeruginosa Pseudomonas_putida_KT2440 Pyrenophora_tritici_repentis_M4 * Saccharomyces_cerevisiae Schistosoma_mansoni Staphylococcus_aureus_COL Streptococcus_pneumoniae_D39 Streptomyces_coelicolor Sulfolobus_solfataricus_P2 Synechococcus_CC9311 Thermoplasma_acidophilum Trypanosoma_brucei_TREU927 Yersinia_pestis_CO92 bp_Rtps_allmgs * pietro temp

GenSearch

Search your sequence against a wide range of genomes

Gensearch options
E-mail address
Optional job description
Amino acid sequence
Choose 1 or more genomes to search (ctrl-click or cmd-click)	Agrobacterium_tumefaciens_C58_Cereon Aplysia_californica Arabidopsis_thaliana Archaeon_GW2011_AR3 Archaeon_GW2011_AR5 Archaeon_GW2011_AR17 Autotransporters Bacillus_subtilis Bartonella_henselae_Houston-1 Bdellovibrio_bacteriovorus Bodo_saltans Caenorhabditis_elegans_WS244 Caenorhabditis_elegans.WS220.66 Caulobacter_crescents Clostridium_difficile Corynebacterium_diphtheriae Desulfitobacterium_hafniense_Y51 Drosophila_melanogaster Enterobacteria_phage_T4 Escherichia_coli_K12 Francisella_novicida_U112 GiardiaDB-37 Homo_sapiens Lactobacillus_casei_ATCC_334 Leishmania_major Listeria_monocytogenes Mus_musculus Mycobacterium_tuberculosis_CDC1551 Nanoarchaeota_archaeon_SCGC_AAA011-K22 Nanoarchaeota_archaeon_SCGC_AAA011-L22 Nanoarchaeota_SCGC_G17_aa Nanoarchaeote_nst1_aa Nanoarchaeum_equitans_aa Neisseria_meningitidis_MC58 Plasmodium_falciparum Pseudomonas_aeruginosa Pseudomonas_putida_KT2440 Saccharomyces_cerevisiae Schistosoma_mansoni Staphylococcus_aureus_COL Streptococcus_pneumoniae_D39 Streptomyces_coelicolor Sulfolobus_solfataricus_P2 Synechococcus_CC9311 Thermoplasma_acidophilum Trypanosoma_brucei_TREU927 Yersinia_pestis_CO92

Other Resources

Missense3D Portal: a suite of resources for the analysis of amino acid substitutions in proteins

GWYRE: contains modeled and experimentally determined structures of human proteins and protein complexes, annotated by phenotypic effects of genetic mutations.

Cambridge 2019 Workshop | Older Workshops | Phyre2 paper

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Phyre is now FREE for commercial users!

All images and data generated by Phyre2 are free to use in any publication with acknowledgement

Accessibility Statement

Please cite: The Phyre2 web portal for protein modeling, prediction and analysis
Kelley LA et al. Nature Protocols 10, 845-858 (2015) [paper] [Citation link]
© Structural Bioinformatics Group, Imperial College, London Michael Sternberg   Disclaimer Terms and Conditions		Phyre2 is part of Genome3D