Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as fire) are free web-based services for protein structure prediction. Phyre...

aa, and 335-346 aa were identified with high confidence using CFSSP and Phyre2. Of all the predicted alpha helices, three alpha helices at 5-15 aa, 189-195...

and 92 to 100 are predicted with the highest confidence using CFSSP and Phyre2. A model predicted by I-TASSER shows that the tertiary structure of human...

I-TASSER, and Phyre2 models all predict that the secondary structure of TMEM101 is predominately composed of alpha helices. The Phyre2 prediction is presented...

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (June 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

Structure of part of ZNF837 as predicted by Phyre2. The structure matches with 99.9% confidence to 37% of the sequence....

PHYRE2 prediction of secondary and tertiary structure for TMEM267...

Cycle The approximate 3D structure of CYC protein generated with Phyre2. The protein sequence information was obtained from the UniProt database. Identifiers...

amino acids 14-32 within the protein. However, structure prediction tool Phyre2 predicts that the protein's transmembrane domain resides on amino acids...

FoldX Energy calculations and protein design Downloadable program Phyre, Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio...

proteins were analyzed to identify structural similarities. According to PHYRE2, SBK3's sequence is similar to that of the F chain of the α subunit of IκB...

2020-05-04. "EMBOSS: pepwheel". www.bioinformatics.nl. Retrieved 2020-05-01. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2020-05-05...

performed by using PRBI database, Phyre2, and I-TASSER. The secondary structure prediction of ZCCHC18 was analyzed by Phyre2. The tertiary structure was predicted...

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (June 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

function prediction". zhanglab.ccmb.med.umich.edu. Retrieved May 2, 2020. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved May 2...

between amino acids 610-655 was predicted to be a coiled coil motif. A Phyre2 protein structure prediction suggested that the first 200 residues of c10orf76...

also significantly different from profile-based methods (e.g., HHPred and Phyre2) in that RaptorX excels at modeling of protein sequences without a large...

Retrieved 2022-07-29. www.sbg.bio.ic.ac.uk http://www.sbg.bio.ic.ac.uk/~phyre2/html/. Retrieved 2022-07-29. {{cite web}}: Missing or empty |title= (help)...

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (June 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

secondary structure consist primarily of alpha helices and coiled coils. Phyre2 also predicted C16orf78 is primarily helical, but 253 of 265 amino acids...

and variant X1. It is phenylalanine rich, and found in the cell membrane. Phyre2 extrapolated the following 3D secondary structure with 100% certainty after...

A prediction of secondary structure of a portion of c2orf81 generated by Phyre2....

model the predicted structure of the c14orf119 protein. Shown in Figure 1, Phyre2 created a model for the predicted structure of 106 (out of a total of 140)...

3-D rendering of SMIM14 protein via Phyre2...

structures Variant effect predictor, UniProt, Protein Data Bank, SIFTS, Phyre2 for predicted structures http://phyrerisk.bc.ic.ac.uk/home Missense3D Reports...

Structure Visualization". dog.biocuckoo.org. Retrieved 2019-05-02. Kelley L. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-04-22...

with the most distant homolog available, that of Trichoplax adhearens. Phyre2 was used to predict protein secondary structure of human FAM46C and trichoplax...

programs at Biology Workbench were compared to the results obtained using Phyre2. Since these programs are predictive and rely on different algorithms, each...

7 May 2018. Retrieved 23 April 2018. "GOR4". Retrieved 23 April 2018. "PHYRE2". Retrieved 23 April 2018. "SIB Motif Scan". Archived from the original...

S2CID 17819277. "SDSC Biology Workbench". workbench.sdsc.edu. Retrieved 2016-02-28. "Phyre2".[permanent dead link] "I-TASSER Protein Structure & Function Predictions"...

dundee.ac.uk/jpred/ Ali2D https://omictools.com/ali2d-tool Phyre2 http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index SIB MyHits MotifScan https://myhits...

consist of alpha helices, extended strands, random coils and beta turns. The Phyre2 server provided a predicted human protein structure that indicated domains...

structural similarity to a viral RNA Polymerase binding protein was predicted by Phyre2. This structure is found at the very end of the protein between amino acids...

Using Phyre2, Ali2D, and I-TASSER predicted that the FAM214B secondary structure composed of mostly beta sheets and one alpha helix. Phyre2 prediction...

doi:10.1073/pnas.0900604106. PMC 2695404. PMID 19520826. Kelley, Lawrence. "PHYRE2 Protein Fold Recognition Server". sbg.bio.ic.ac.uk. Retrieved 2018-05-07...

Protein Structure Database". alphafold.ebi.ac.uk. Retrieved 2024-11-30. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2024-12-04...

some random coil. Ali2D Secondary Structure for CCDC121 protein isoform 1 Phyre2 Tertiary structure prediction for CCDC121 protein isoform 1 CCDC121 contains...

Server". www.compbio.dundee.ac.uk. Retrieved 2018-04-24. Kelley, Lawrence. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2018-04-24...

residues long, so called WD40. The structure of CORO6 is predicted by using Phyre2 program. It is similar to the crystal structure of murine coronin-1. 390...

needs referencing to figures and experimental demonstration] The program Phyre2 was used to construct predictions of both the conserved domain regions NIDO...

group, particularly Lawrence Kelley, have developed the widely used Phyre/Phyre2 web server for protein structure prediction. This web resource has been...

strands, beta turns, and Random coils. Both Tertiary structures predicted by Phyre2 and the SWISS model show that C1orf94 is a monomer. According to I-TASSER...

corresponded with the secondary structure and 3D structure predictions made by PHYRE2 MEGF8 is predicted to contain several different types of features, domains...

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (June 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

OBPgp279 Predicted structure of OPBgp279 from Phyre2. Homology model based on 4OK7. Identifiers Organism Pseudomonas phage OBP Symbol OBP_279 UniProt G9I9L2...

α-helix from amino acid 38 to 52 of PRR16 determined by PHYRE2...

ExPASy Bioinformatics Resource Portal http://www.expasy.org/proteomics PHYRE2 - STRING - Known and Predicted Protein-Protein Interactions http://string-db...

Predicted Structure of Stat-1 and Stat3b-like DNA binding domains in NBPF1 using Phyre2...

structure of CCDC142 contains only α-helices as predicted by the Quick2D and Phyre2 programs . It is predicted that CCDC142 contains eight conserved α-helices...

(2): 365–71. doi:10.1016/j.ajhg.2012.06.012. PMC 3415545. PMID 22818856. "Phyre2". Structural Bioinformatics Group.[permanent dead link] "ExPASy: SIB Bioinformatics...

| mfold.rit.albany.edu". unafold.rna.albany.edu. Retrieved 2019-04-17. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-04-20...

25, 2019, from https://swissmodel.expasy.org/repository/uniprot//Q8IXR5 "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-04-22...

beta sheet regions and only one highly predicted alpha helix region. The PHYRE2 analysis of 65 residues of CCDC94, 20% of the entire amino acid sequence...

function prediction". zhanglab.ccmb.med.umich.edu. Retrieved 2020-12-14. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2020-12-14...

Statistical Analysis of Protein Sequences". EMBL-EBI -SAPS. 2019-05-05. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-05-04...

original on 2016-05-14. Retrieved 2016-05-05. Lawrence Kelley (2011-02-14). "PHYRE2 Protein Fold Recognition Server". Sbg.bio.ic.ac.uk. Retrieved 2016-05-05...

Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2016-05-03. Kelley L. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2016-05-03...

tertiary structure and can be visualized using the predicted structure from Phyre2. Shown on the structure are the two known phosphorylated sites and one ubiquitylation...

Domains. Prosite. 9 May 2015. Retrieved 9 May 2015. Kelley L, Sternberg M. "Phyre2". Structural Bioinformatics Group. Retrieved 12 April 2015. Källberg M,...

Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2020-12-19. Kelley L. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2020-12-19...

Kelley, LA; Mezulis, S; Yates, CM; Wass, MN; Sternberg, MJ (2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

of the mature protein is 70.0 kdal with an isoelectric point of 5.494. PHYRE2 protein tertiary structure tool suggests that RUFY2 has 15 alpha helices...

residues 19 to 152 with 97.3% confidence with 56% coverage obtained using Phyre2. The red-to-blue color gradation indicates the N- to C-terminus directionality...

2020-12-19. "ELM - Search the ELM resource". elm.eu.org. Retrieved 2020-12-19. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2020-12-19...

sapiens (human) ]". U.S. National Library of Medicine. Retrieved 4 May 2013. "Phyre2". Retrieved 18 April 2013.[permanent dead link] Blatch GL, Lässle M (November...

Retrieved 2020-02-03. "GTEx Portal". gtexportal.org. Retrieved 2020-02-03. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2020-04-29...

structure with the highest confidence of human ccdc190 based on the results of Phyre2. Two coiled-coil domains can be identified from the figure. Regions of red...

II Prediction". psort.hgc.jp. Retrieved 2018-04-22. Kelley, Lawrence. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2018-05-06...

pairs. The figure "FAM200C Predicted Secondary Structure" 1 and 2 provide a Phyre2.2 model prediction of FAM200C's secondary structure. Model indicates secondary...

of the tertiary structure predicted by the I-TASSER program. The program Phyre2 also predicts the protein to be made up primarily of alpha helices. After...

Predictions". Zhang Lab. Kelley, L., Mezulis, S., Yates, C. et al. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10...

analysis, two alpha-helical segments were predicted. Predictive models made by Phyre2 and SWISS-Model have shown two alpha-helical domains with a bend between...

"CFSSP". CFSSP: Chou & Fasman Secondary Structure Prediction Server. "Phyre2". Phyre 2 Protein Fold Recognition Server.[permanent dead link] "UCSC Genome...

was predicted with 100% confidence by the structure predicting program Phyre2. The most notable proteins that interact with human WDR90 are predicted...

Yates, Christopher M.; Wass, Mark N.; Sternberg, Michael J. E. (2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

statistics". isoelectricpointdb.org. Retrieved 2017-04-30. Kelley, Lawrence. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2017-05-05...

tertiary structure on the basis of homology to published 3d structures via Phyre2 and NCBI structure. The promoter for human SOGA2 is below. The EST profile...

prediction". zhanglab.ccmb.med.umich.edu. Zhang Lab, University of Michigan. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Structural Bioinformatics...

tertiary structure of Human C18orf12 was generated by AlphaFold and annotated with iCn3D. The FhuA protein tertiary structure was generated with Phyre2....

from the original on 2003-08-11. Retrieved 2015-05-09. Kelley, Lawrence. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2015-05-09...

terminus (residues 12-51) Secondary structure prediction tools such as Ali2D, Phyre2, and i-Tasser all predict that the C11orf49 protein is mostly composed of...

function in C8orf34. The structure prediction and analysis application Phyre2 reported that a portion of C8orf34 has close structural similarity with...

Archived from the original on 2016-08-13. Retrieved 2016-05-10. Kelley L. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2016-05-09...

"Kegg T01001: 84229". "Multiple sequence alignment: Strap". "Redirecting to Phyre2". Archived from the original on 30 April 2017. Retrieved 9 May 2010. "Clustal...

Bioinformatics Resource Portal - Categories". www.expasy.org. Retrieved 2020-05-03. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2020-04-30...

structure prediction. "PROSITE". prosite.expasy.org. Retrieved 2020-05-01. "PHYRE2". Protein Homology/analogy recognition engine. "Genomatix: Retrieve and...

"FAM221B Homo sapiens Isoform X2". "FAM221B Homo sapiens Isoform X3". "PHYRE2 secondary structure prediction for FAM221B".[permanent dead link] "MyHits...

149 to 172. There is a cross-program consensus between GOR4, CFSSP, and PHYRE2 that the protein structure contains mostly coiled regions and alpha helices...

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (June 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

composed of 81% alpha helices, 25.6% beta sheets, and 17.2% turns. Using Phyre2, 284 residues (45% of GOLGA8H) was modeled with 97.8% confidence by the...

structure and function prediction". zhanggroup.org. Retrieved 2023-12-15. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2023-12-15...

For Undefined". Sbg.Bio.Ic.Ac.Uk, 2019, http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/607daef47ac621bf/summary.html Archived 2019-08-04 at the Wayback...

seven beta-sheet regions and one alpha helix region and according to the Phyre2 program, there is 100% confidence that the structure of 95% of the C1orf123...

Biotechnology Information, U.S. National Library of Medicine. Kelley L. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2017-05-07...

(SMIM11A)". research.bioinformatics.udel.edu. "NetPhos 3.1 Server". cbs.dtu.dk. "Phyre2 Results". sbg.bio.ic.ac.uk. "TMHHM Server". cbs.dtu.dk. "STRING FAM165B"...

R.; Islam, Suhail A.; David, Alessia; Sternberg, Michael J.E. (2025). "Phyre2.2: A Community Resource for Template-based Protein Structure Prediction"...

Figure 1. A diagram of the UBact Pup homolog. Phyre2 server was used to predict the structure of the UBact Pup homolog from the bacterium Methylacidiphilum...

1177/1533033818811143. PMC 6259056. PMID 30482097. "Phyre 2 Results for PANO1_phyre2". www.sbg.bio.ic.ac.uk. Archived from the original on 2021-08-01. Retrieved...

domains, and alpha-helices. Tertiary structures of TEX55 was generated using Phyre2. The C-terminus, which is highly conserved, was calculated to have a 30...

- NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-10-20. Kelley, Lawrence. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2022-12-14...

PMID 28472402. Powell HR, Islam SA, David A, Sternberg MJ (August 2025). "Phyre2.2: A Community Resource for Template-based Protein Structure Prediction"...

Tertiary structure of IFFO1 protein as predicted by PHYRE2 program...

FAM155B[permanent dead link] ] EMBL-EBI, SAPS: FAM155B ] InterProScan: FAM155B ] Phyre2: FAM155B ] UCSC Genome Browser: FAM155B Genomatix, Promoter: FAM155B Quickfold:...

Genome Bioinformatics". "ExPASy N-glycosylation". "ExPASy Phosphorylation". "ExPASy Phyre2". "ExPASy SOSUI". Archived from the original on 2004-03-20....

secondary structure prediction". npsa-prabi.ibcp.fr. Retrieved 2019-04-21. "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-05-03...

"Uncharacterized protein CXorf65". Alphafold. "Job ID: c2f0c773ba05d9ac". Phyre2. Archived from the original on 2022-12-17. Retrieved 2022-12-17. "ELM Functional...

multiple names: authors list (link) "Proposed Tertiary Structure for ERICH4". Phyre2.[dead link] "Proposed Tertiary Structure for ERICH4". I-TASSER.[dead link]...

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (June 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols...

acids 96–97. The tertiary structure for C16orf86 PDB file was taken from Phyre2 and I-Tasser. The PDB files were put into EZmol bioinformatics tool to create...

transmembrane protein. The structure of FAM98A was predicted with the program Phyre2. The N-terminal region contains several alpha helices, and a C-terminal...