The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
JPred4: a protein secondary structure prediction server
Open accessAbstract
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
UniRef: comprehensive and non-redundant UniProt reference clusters
Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R., & Wu, C. H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm098 · Cited by 1,613
Protein 3D Structure Computed from Evolutionary Sequence Variation
Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144
TargetDB: a target registration database for structural genomics projects
Chen, L., Oughtred, R., Berman, H. M., & Westbrook, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth300 · Cited by 176 · cited 3×
“(1) Illustration of a single sequence job submission secondary structure prediction results summary email with link to full result details (2).”
Background
Cited by
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature · doi:10.1038/s41586-020-2286-9 · Cited by 4,405
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,761
ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning
Elnaggar, A., Heinzinger, M., Dallago, C., Rehawi, G., Wang, Y., Jones, L., Gibbs, T., Feher, T., Angerer, C., Steinegger, M., et al. (2022) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2021.3095381 · Cited by 2,329
Khalifa, A. A. Z., Ichikawa, M., Dai, D., Kubo, S., Black, C. S., Peri, K., McAlear, T. S., Veyron, S., Yang, S. K., Vargas, J., et al. (2020) · eLife · doi:10.7554/elife.52760 · Cited by 1,676
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Minakhin, L., Joung, J., Konermann, S., Severinov, K., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.008 · Cited by 1,209
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Wang, S., Sun, S., Li, Z., Zhang, R., & Xu, J. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005324 · Cited by 931
Evaluating Protein Transfer Learning with TAPE
Rao, R., Bhattacharya, N., Thomas, N., Duan, Y., Chen, X., Canny, J., Abbeel, P., & Song, Y. S. (2019) · doi:10.1101/676825 · Cited by 719
Modeling the language of life – Deep Learning Protein Sequences
Heinzinger, M., Elnaggar, A., Wang, Y., Dallago, C., Nechaev, D., Matthes, F., & Rost, B. (2019) · doi:10.1101/614313 · Cited by 606
Modeling aspects of the language of life through transfer-learning protein sequences
Heinzinger, M., Elnaggar, A., Wang, Y., Dallago, C., Nechaev, D., Matthes, F., & Rost, B. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3220-8 · Cited by 606
Human gut bacteria produce ΤΗ17-modulating bile acid metabolites
Paik, D., Yao, L., Zhang, Y., Bae, S., D’Agostino, G. D., Zhang, M., Kim, E., Franzosa, E. A., Avila-Pacheco, J., Bisanz, J. E., et al. (2022) · Nature · doi:10.1038/s41586-022-04480-z · Cited by 594
Structure of the Decorated Ciliary Doublet Microtubule
Ma, M., Stoyanova, M., Rademacher, G., Dutcher, S. K., Brown, A., & Zhang, R. (2019) · Cell · doi:10.1016/j.cell.2019.09.030 · Cited by 290
In-cell architecture of an actively transcribing-translating expressome
O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284
Proteome-wide analysis of chaperone-mediated autophagy targeting motifs
Kirchner, P., Bourdenx, M., Madrigal-Matute, J., Tiano, S., Diaz, A., Bartholdy, B. A., Will, B., & Cuervo, A. M. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000301 · Cited by 257
The SARS-CoV-2 Spike variant D614G favors an open conformational state
Mansbach, R. A., Chakraborty, S., Nguyen, K., Montefiori, D. C., Korber, B., & Gnanakaran, S. (2021) · Science Advances · doi:10.1126/sciadv.abf3671 · Cited by 206
Architecture of the human GATOR1 and GATOR1–Rag GTPases complexes
Shen, K., Huang, R. K., Brignole, E. J., Condon, K. J., Valenstein, M. L., Chantranupong, L., Bomaliyamu, A., Choe, A., Hong, C., Yu, Z., et al. (2018) · Nature · doi:10.1038/nature26158 · Cited by 192
Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V., & Koonin, E. V. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1803440115 · Cited by 169
The structure of human thyroglobulin
Coscia, F., Taler-Verčič, A., Chang, V. T., Sinn, L., O’Reilly, F. J., Izoré, T., Renko, M., Berger, I., Rappsilber, J., Turk, D., et al. (2020) · Nature · doi:10.1038/s41586-020-1995-4 · Cited by 147
Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex
Wieczorek, M., Urnavicius, L., Ti, S.-C., Molloy, K. R., Chait, B. T., & Kapoor, T. M. (2020) · Cell · doi:10.1016/j.cell.2019.12.007 · Cited by 136
rawMSA: End-to-end Deep Learning using raw Multiple Sequence Alignments
Mirabello, C., & Wallner, B. (2019) · PLOS ONE · doi:10.1371/journal.pone.0220182 · Cited by 105
Mechanism of cargo recognition by retromer-linked SNX-BAR proteins
Yong, X., Zhao, L., Deng, W., Sun, H., Zhou, X., Mao, L., Hu, W., Shen, X., Sun, Q., Billadeau, D. D., et al. (2020) · PLOS Biology · doi:10.1371/journal.pbio.3000631 · Cited by 93
Diffusing protein binders to intrinsically disordered proteins
Liu, C., Wu, K., Choi, H., Han, H. L., Zhang, X., Watson, J. L., Ahn, G., Zhang, J. Z., Shijo, S., Good, L. L., et al. (2025) · Nature · doi:10.1038/s41586-025-09248-9 · Cited by 79
Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases
Junqueira Alves, C., Yotoko, K., Zou, H., & Friedel, R. H. (2019) · Scientific Reports · doi:10.1038/s41598-019-38512-y · Cited by 72
Kouba, T., Vogel, D., Thorkelsson, S. R., Quemin, E. R. J., Williams, H. M., Milewski, M., Busch, C., Günther, S., Grünewald, K., Rosenthal, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27305-5 · Cited by 50
Structures and activation mechanism of the Gabija anti-phage system
Li, J., Cheng, R., Wang, Z., Yuan, W., Xiao, J., Zhao, X., Du, X., Xia, S., Wang, L., Zhu, B., et al. (2024) · Nature · doi:10.1038/s41586-024-07270-x · Cited by 46
Khusnutdinova, A. N., Batyrova, K. A., Brown, G., Fedorchuk, T., Chai, Y. S., Skarina, T., Flick, R., Petit, A., Savchenko, A., Stogios, P., et al. (2023) · The FEBS Journal · doi:10.1111/febs.16903 · Cited by 40
Sequence clustering confounds AlphaFold2
Schafer, J. W., Lee, M., Chakravarty, D., Thole, J. F., Chen, E. A., & Porter, L. L. (2025) · Nature · doi:10.1038/s41586-024-08267-2 · Cited by 38
Islam, S. T., Jolivet, N. Y., Cuzin, C., Belgrave, A. M., My, L., Fleuchot, B., Faure, L. M., Mahanta, U., Kezzo, A. A., Saïdi, F., et al. (2023) · Science Advances · doi:10.1126/sciadv.abq0619 · Cited by 38
Human Sialidase Neu3 is S-Acylated and Behaves Like an Integral Membrane Protein
Rodriguez-Walker, M., & Daniotti, J. L. (2017) · Scientific Reports · doi:10.1038/s41598-017-04488-w · Cited by 36
PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance
Parashara, P., Medina-Pritchard, B., Abad, M. A., Sotelo-Parrilla, P., Thamkachy, R., Grundei, D., Zou, J., Spanos, C., Kumar, C. N., Basquin, C., et al. (2024) · Science · doi:10.1126/science.ado8270 · Cited by 36
Formation of a structurally-stable conformation by the intrinsically disordered MYC:TRRAP complex
Feris, E. J., Hinds, J. W., & Cole, M. D. (2019) · PLOS ONE · doi:10.1371/journal.pone.0225784 · Cited by 29
The Charged Linker Modulates the Conformations and Molecular Interactions of Hsp90
López, A., Elimelech, A. R., Klimm, K., & Sattler, M. (2021) · ChemBioChem · doi:10.1002/cbic.202000699 · Cited by 30
The human protein haptoglobin inhibits IsdH-mediated heme-sequestering by Staphylococcus aureus
Mikkelsen, J. H., Runager, K., & Andersen, C. B. F. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.011612 · Cited by 27
Zuber, P. K., Daviter, T., Heißmann, R., Persau, U., Schweimer, K., & Knauer, S. H. (2022) · eLife · doi:10.7554/elife.76630 · Cited by 29
Rescue of Escherichia coli auxotrophy by de novo small proteins
Babina, A. M., Surkov, S., Ye, W., Jerlström-Hultqvist, J., Larsson, M., Holmqvist, E., Jemth, P., Andersson, D. I., & Knopp, M. (2023) · eLife · doi:10.7554/elife.78299 · Cited by 24
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322003576 · Cited by 24
Schäffer, D. E., Iyer, L. M., Burroughs, A. M., & Aravind, L. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00034 · Cited by 20
Yang, Z., & Tsui, S. K.-W. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00262 · Cited by 19
A cytoplasmic chemoreceptor and reactive oxygen species mediate bacterial chemotaxis to copper
Louis, G., Cherry, P., Michaux, C., Rahuel-Clermont, S., Dieu, M., Tilquin, F., Maertens, L., Van Houdt, R., Renard, P., Perpete, E., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105207 · Cited by 17
Kahveci-Türköz, S., Bläsius, K., Wozniak, J., Rinkens, C., Seifert, A., Kasparek, P., Ohm, H., Oltzen, S., Nieszporek, M., Schwarz, N., et al. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04783-y · Cited by 17
Kors, S., Schuster, M., Maddison, D. C., Kilaru, S., Schrader, T. A., Costello, J. L., Islinger, M., Smith, G. A., & Schrader, M. (2024) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2024.119843 · Cited by 12
Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes
Meyer, B. H., Adam, P. S., Wagstaff, B. A., Kolyfetis, G. E., Probst, A. J., Albers, S. V., & Dorfmueller, H. C. (2022) · eLife · doi:10.7554/elife.67448 · Cited by 12
Structure of the Human Signal Peptidase Complex Reveals the Determinants for Signal Peptide Cleavage
Liaci, A. M., Steigenberger, B., Tamara, S., de Souza, P. C. T., Gröllers-Mulderij, M., Ogrissek, P., Marrink, S. J., Scheltema, R. A., & Förster, F. (2020) · doi:10.1101/2020.11.11.378711 · Cited by 10
Tan, Y., Wang, C., Schneider, T., Li, H., de Souza, R. F., Tang, X., Swisher Grimm, K. D., Hsieh, T.-F., Wang, X., Li, X., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00509-21 · Cited by 10
Sonntag, T., Omi, S., Andreeva, A., Valotteau, C., Eichelbrenner, J., Chisholm, A. D., Ward, J. D., & Pujol, N. (2025) · PLOS Genetics · doi:10.1371/journal.pgen.1011593 · Cited by 9
Evolution of g-type lysozymes in metazoa: insights into immunity and digestive adaptations
Mukherjee, K., & Moroz, L. L. (2024) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2024.1487920 · Cited by 7
Kramer, D. A., Narvaez-Ortiz, H. Y., Patel, U., Shi, R., Shen, K., Nolen, B. J., Roche, J., & Chen, B. (2023) · eLife · doi:10.7554/elife.88492 · Cited by 7
PS4: A Next-Generation Dataset for Protein Single-Sequence Secondary Structure Prediction
Peracha, O. (2024) · BioTechniques · doi:10.2144/btn-2023-0024 · Cited by 7
The topological properties of the protein universe
Madsen, C. D., Barbensi, A., Zhang, S. Y., Ham, L., David, A., Pires, D. E. V., & Stumpf, M. P. H. (2025) · Nature Communications · doi:10.1038/s41467-025-61108-2 · Cited by 7
Molecular structure of the ESCRT-III-based archaeal CdvAB cell division machinery
Drobnič, T., Salzer, R., Nierhaus, T., Jiang, M. K. X., Bellini, D., Steindorf, A., Albers, S.-V., Baum, B., & Löwe, J. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2525941123 · Cited by 5
Shishir, T. A., Jannat, T., & Naser, I. B. (2022) · doi:10.1101/2022.02.21.481269 · Cited by 5
Dudziak, A., Pleuger, R., Schmidt, J., Hamm, F., Tendulkar, S., Jänen, K., Vetter, I. R., Singh, S., Fischböck, J., Herzog, F., et al. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00437-w · Cited by 4
LC8 enhances 53BP1 foci through heterogeneous bridging of 53BP1 oligomers
Howe, J., Walker, D., Tengler, K., Sonpatki, M., Reardon, P. N., Leung, J. W., & Barbar, E. J. (2025) · eLife · doi:10.7554/elife.102179 · Cited by 4
Cryo‐EM structures of multiple‐peptide resistance factor ( MprF ) from Pseudomonas aeruginosa
Jha, S., & Vinothkumar, K. R. (2026) · The FEBS Journal · doi:10.1111/febs.70519 · Cited by 1
Volkening, J. D., Spatz, S. J., Garcia, M., Ross, T. A., Maekawa, D. A., Rosenthal, K. S., Zamora, A. C., Skipper, A., Blakey, J. R., & Paudel, R. (2025) · PLOS Pathogens · doi:10.1371/journal.ppat.1013219 · Cited by 1
Metadata
- Authors
- Drozdetskiy, A., Cole, C., Procter, J., & Barton, G. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-04-16
- Volume
- 43
- Issue
- W1
- Pages
- W389-W394
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2029476353
- Cited by
- 1,744
- References
- 4
- FWCI
- 59.44
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
