Microproteins: a 3D protein structure prediction analysis

References

• 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., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25(1), 25–29. https://doi.org/10.1038/75556
   PubMed Web of Science ®Google Scholar
• Biro, J. C. (2007). The Proteomic Code: A molecular recognition code for proteins. Theoretical Biology & Medical Modelling, 4(1), 45. https://doi.org/10.1186/1742-4682-4-45
   PubMedGoogle Scholar
• Brooks, D. J., Fresco, J. R., Lesk, A. M., & Singh, M. (2002). Evolution of amino acid frequencies in proteins over deep time: Inferred order of introduction of amino acids into the genetic code. Molecular Biology and Evolution, 19(10), 1645–1655. https://doi.org/10.1093/oxfordjournals.molbev.a003988
   PubMed Web of Science ®Google Scholar
• Heinig, M., & Frishman, D. (2004). STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Research, 32(Web Server issue), W500–2. https://doi.org/10.1093/nar/gkh429
   PubMedGoogle Scholar
• Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., & Xu, J. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 7(8), 1511–1522. https://doi.org/10.1038/nprot.2012.085
   PubMed Web of Science ®Google Scholar
• Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., & Xu, J. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 7(8), 1511–1522. https://doi.org/10.1038/nprot.2012.085
   PubMed Web of Science ®Google Scholar
• Kim, D. E., Chivian, D., & Baker, D. (2004). Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research, 32(Web Server issue), W526–W31. https://doi.org/10.1093/nar/gkh468
   PubMed Web of Science ®Google Scholar
• Kim, D. E., Chivian, D., & Baker, D. (2004). Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research, 32(Web Server issue), W526–W31. https://doi.org/10.1093/nar/gkh468
   PubMed Web of Science ®Google Scholar
• Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2019). Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins: Structure, Function, and Bioinformatics, 87(12), 1011–1020. https://doi.org/10.1002/prot.25823
   PubMed Web of Science ®Google Scholar
• Kryshtafovych, A., Venclovas, Č., Fidelis, K., & Moult, J. (2005). Progress over the first decade of CASP experiments. Proteins: Structure, Function, and Bioinformatics, 61(S7), 225–236. https://doi.org/10.1002/prot.20740
   PubMedGoogle Scholar
• Ma, J., Ward, C. C., Jungreis, I., Slavoff, S. A., Schwaid, A. G., Neveu, J., Budnik, B. A., Kellis, M., & Saghatelian, A. (2014). Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. Journal of Proteome Research, 13(3), 1757–1765. https://doi.org/10.1021/pr401280w
   PubMed Web of Science ®Google Scholar
• Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T., & Tramontano, A. (2014). Critical assessment of methods of protein structure prediction (CASP)—round x. Proteins: Structure, Function, and Bioinformatics, 82(S2), 1–6. https://doi.org/10.1002/prot.24452
   PubMedGoogle Scholar
• Moult, J., Fidelis, K., Zemla, A., & Hubbard, T. (2001). Critical assessment of methods of protein structure prediction (CASP): Round IV. Proteins: Structure, Function, and Genetics, 45(S5), 2–7. https://doi.org/10.1002/prot.10054
   PubMedGoogle Scholar
• Rathore, A., Martinez, T. F., Chu, Q., & Saghatelian, A. (2018). Small, but mighty? Searching for human microproteins and their potential for understanding health and disease. Expert Review of Proteomics, 15(12), 963–965. https://doi.org/10.1080/14789450.2018.1547194
   PubMed Web of Science ®Google Scholar
• Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738. https://doi.org/10.1038/nprot.2010.5
   PubMed Web of Science ®Google Scholar
• Saghatelian, A., & Couso, J. P. (2015). Discovery and characterization of smORF-encoded bioactive polypeptides. Nature Chemical Biology, 11(12), 909–916. https://doi.org/10.1038/nchembio.1964
   PubMed Web of Science ®Google Scholar
• Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. PLOS One, 6(7), e21800. https://doi.org/10.1371/journal.pone.0021800
   PubMed Web of Science ®Google Scholar
• Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J., & von Mering, C. (2015). STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res, 43(Database issue), D447–D52. https://doi.org/10.1093/nar/gku1003
   PubMed Web of Science ®Google Scholar
• Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., Jensen, L. J., & Mering, C. v. (2019). STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1), D607–D13. https://doi.org/10.1093/nar/gky1131
   PubMed Web of Science ®Google Scholar
• Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., Jensen, L. J., & von Mering, C. (2017). The STRING database in 2017: Quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research, 45(D1), D362–d8. https://doi.org/10.1093/nar/gkw937
   PubMed Web of Science ®Google Scholar
• Tanner, J. J. (2016). Empirical power laws for the radii of gyration of protein oligomers. Acta Crystallographica. Section D, Structural Biology, 72(Pt 10), 1119–1129. https://doi.org/10.1107/S2059798316013218
   PubMedGoogle Scholar
• Vacic, V., Uversky, V. N., Dunker, A. K., & Lonardi, S. (2007). Composition Profiler: A tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics, 8(1), 211. https://doi.org/10.1186/1471-2105-8-211
   PubMed Web of Science ®Google Scholar
• Wu, C. H., Apweiler, R., Bairoch, A., Natale, D. A., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Mazumder, R., O'Donovan, C., Redaschi, N., & Suzek, B. (2006). The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Research, 34(Database issue), D187–91. https://doi.org/10.1093/nar/gkj161
   PubMed Web of Science ®Google Scholar
• Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/10.1038/nmeth.3213
   PubMed Web of Science ®Google Scholar
• Yang Zhang Lab (XXXX) I-TASSER FAQ, #10. https://zhanglab.ccmb.med.umich.edu/I-TASSER/FAQ.html#10.
   Google Scholar
• Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40.
   PubMed Web of Science ®Google Scholar