The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
PredictProtein—an open resource for online prediction of protein structural and functional features
Open accessAbstract
PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein-protein binding sites (ISIS2), protein-polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org.
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
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
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
SignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) · Nature Methods · doi:10.1038/nmeth.1701 · Cited by 8,847
Predicting coiled coils from protein sequences.
Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953
A large-scale evaluation of computational protein function prediction
Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2340 · Cited by 1,028
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Zimmermann, L., Stephens, A., Nam, S.-Z., Rau, D., Kübler, J., Lozajic, M., Gabler, F., Söding, J., Lupas, A. N., & Alva, V. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.12.007 · Cited by 2,522
Meltome atlas—thermal proteome stability across the tree of life
Jarzab, A., Kurzawa, N., Hopf, T., Moerch, M., Zecha, J., Leijten, N., Bian, Y., Musiol, E., Maschberger, M., Stoehr, G., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0801-4 · Cited by 281
Powis, K., Zhang, T., Panchaud, N., Wang, R., Virgilio, C. D., & Ding, J. (2015) · Cell Research · doi:10.1038/cr.2015.86 · Cited by 80
Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface
Jenni, S., & Harrison, S. C. (2018) · Science · doi:10.1126/science.aar6436 · Cited by 72
Oleinik, N., Kim, J., Roth, B. M., Selvam, S. P., Gooz, M., Johnson, R. H., Lemasters, J. J., & Ogretmen, B. (2019) · Science Advances · doi:10.1126/sciadv.aax1978 · Cited by 68
Metadata
- Authors
- Yachdav, G., Kloppmann, E., Kajan, L., Hecht, M., Goldberg, T., Hamp, T., Hönigschmid, P., Schafferhans, A., Roos, M., Bernhofer, M., Richter, L., Ashkenazy, H., Punta, M., Schlessinger, A., Bromberg, Y., Schneider, R., Vriend, G., Sander, C., Ben-Tal, N., & Rost, B.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-05-05
- Volume
- 42
- Issue
- W1
- Pages
- W337-W343
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2154479185
- Cited by
- 595
- References
- 6
- FWCI
- 23.00
- Type
- journal article
- Language
- en
- Open access
- gold
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- The paper
- Yachdav, G., Kloppmann, E., Kajan, L., Hecht, M., Goldberg, T., Hamp, T., Hönigschmid, P., Schafferhans, A., Roos, M., Bernhofer, M., Richter, L., Ashkenazy, H., Punta, M., Schlessinger, A., Bromberg, Y., Schneider, R., Vriend, G., Sander, C., Ben-Tal, N., & Rost, B. (2014). PredictProtein—an open resource for online prediction of protein structural and functional features. Nucleic Acids Research. https://doi.org/10.1093/nar/gku366
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