STOPGAP: an open-source package for template matching, subtomogram alignment and classification

References

First citationBalyschew, N., Yushkevich, A., Mikirtumov, V., Sanchez, R. M., Sprink, T. & Kudryashev, M. (2023). Nat. Commun. 14, 6543.  CrossRef PubMed Google Scholar
First citationBartesaghi, A., Sprechmann, P., Liu, J., Randall, G., Sapiro, G. & Subramaniam, S. (2008). J. Struct. Biol. 162, 436–450.  Web of Science CrossRef PubMed CAS Google Scholar
First citationBeck, M. & Baumeister, W. (2016). Trends Cell Biol. 26, 825–837.  Web of Science CrossRef PubMed Google Scholar
First citationBharat, T. A. M., Russo, C. J., Löwe, J., Passmore, L. A. & Scheres, S. H. W. (2015). Structure, 23, 1743–1753.  Web of Science CrossRef CAS PubMed Google Scholar
First citationCastaño-Díez, D., Kudryashev, M., Arheit, M. & Stahlberg, H. (2012). J. Struct. Biol. 178, 139–151.  Web of Science PubMed Google Scholar
First citationCastaño-Díez, D. & Zanetti, G. (2019). Curr. Opin. Struct. Biol. 58, 68–75.  PubMed Google Scholar
First citationChaillet, M. L., van der Schot, G., Gubins, I., Roet, S., Veltkamp, R. C. & Förster, F. (2023). Int. J. Mol. Sci. 24, 13375.  CrossRef PubMed Google Scholar
First citationChen, S., McMullan, G., Faruqi, A. R., Murshudov, G. N., Short, J. M., Scheres, S. H. W. & Henderson, R. (2013). Ultramicroscopy, 135, 24–35.  Web of Science CrossRef CAS PubMed Google Scholar
First citationCruz-León, S., Majtner, T., Hoffmann, P. C., Kreysing, J. P., Tuijtel, M. W., Schaefer, S. L., Geissler, K., Beck, M., Turoňová, B. & Hummer, G. (2023). bioRxiv, 2023.09.05.556310.  Google Scholar
First citationErdmann, P. S., Hou, Z., Klumpe, S., Khavnekar, S., Beck, F., Wilfling, F., Plitzko, J. M. & Baumeister, W. (2021). Nat. Commun. 12, 5364.  CrossRef PubMed Google Scholar
First citationFernández, J. J., Li, S. & Crowther, R. A. (2006). Ultramicroscopy, 106, 587–596.  Web of Science PubMed Google Scholar
First citationFörster, F., Medalia, O., Zauberman, N., Baumeister, W. & Fass, D. (2005). Proc. Natl Acad. Sci. USA, 102, 4729–4734.  Web of Science PubMed Google Scholar
First citationFrangakis, A. S., Böhm, J., Förster, F., Nickell, S., Nicastro, D., Typke, D., Hegerl, R. & Baumeister, W. (2002). Proc. Natl Acad. Sci. USA, 99, 14153–14158.  CrossRef PubMed CAS Google Scholar
First citationGrant, T. & Grigorieff, N. (2015). eLife, 4, e06980.  Web of Science CrossRef PubMed Google Scholar
First citationGrant, T., Rohou, A. & Grigorieff, N. (2018). eLife, 7, e35383.  Web of Science CrossRef PubMed Google Scholar
First citationHimes, B. A. & Zhang, P. (2018). Nat. Methods, 15, 955–961.  Web of Science CrossRef CAS PubMed Google Scholar
First citationHoffmann, P. C., Kreysing, J. P., Khusainov, I., Tuijtel, M. W., Welsch, S. & Beck, M. (2022). Nat. Commun. 13, 7435.  CrossRef PubMed Google Scholar
First citationHrabe, T., Chen, Y., Pfeffer, S., Kuhn Cuellar, L., Mangold, A.-V. & Förster, F. (2012). J. Struct. Biol. 178, 177–188.  CrossRef CAS PubMed Google Scholar
First citationKhavnekar, S., Erdmann, P. & Wan, W. (2023). Microsc. Microanal. 29, 1020.  CrossRef PubMed Google Scholar
First citationKhavnekar, S., Kelley, R., Waltz, F., Wietrzynski, W., Zhang, X., Obr, M., Tagiltsev, G., Beck, F., Wan, W., Briggs, J., Engel, B., Plitzko, J. & Kotecha, A. (2023). Microsc. Microanal. 29, 961–963.  CrossRef PubMed Google Scholar
First citationKhavnekar, S., Vrbovská, V., Zaoralová, M., Kelley, R., Beck, F., Klumpe, S., Kotecha, A., Plitzko, J. & Erdmann, P. S. (2022). bioRxiv, 2022.06.16.496417.  Google Scholar
First citationKremer, J. R., Mastronarde, D. N. & McIntosh, J. R. (1996). J. Struct. Biol. 116, 71–76.  CrossRef CAS PubMed Web of Science Google Scholar
First citationKühlbrandt, W. (2014). Science, 343, 1443–1444.  Web of Science PubMed Google Scholar
First citationKunz, M. & Frangakis, A. S. (2017). J. Struct. Biol. 197, 114–122.  Web of Science CrossRef PubMed Google Scholar
First citationLacey, S. E., Foster, H. E. & Pigino, G. (2023). Nat. Struct. Mol. Biol. 30, 584–593.  Web of Science CrossRef CAS PubMed Google Scholar
First citationLeigh, K. E., Navarro, P. P., Scaramuzza, S., Chen, W., Zhang, Y., Castaño-Díez, D. & Kudryashev, M. (2019). Methods Cell Biol. 152, 217–259.  CrossRef PubMed Google Scholar
First citationMilicevic, N., Jenner, L., Myasnikov, A., Yusupov, M. & Yusupova, G. (2024). Nature, 625, 393–400.  CrossRef CAS PubMed Google Scholar
First citationNi, T., Frosio, T., Mendonça, L., Sheng, Y., Clare, D., Himes, B. A. & Zhang, P. (2022). Nat. Protoc. 17, 421–444.  CrossRef CAS PubMed Google Scholar
First citationNicastro, D., Schwartz, C., Pierson, J., Gaudette, R., Porter, M. E. & McIntosh, J. R. (2006). Science, 313, 944–948.  Web of Science CrossRef PubMed CAS Google Scholar
First citationPettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). J. Comput. Chem. 25, 1605–1612.  Web of Science CrossRef PubMed CAS Google Scholar
First citationPyle, E. & Zanetti, G. (2021). Biochem. J. 478, 1827–1845.  Web of Science CrossRef CAS PubMed Google Scholar
First citationRangan, R., Khavnekar, S., Lerer, A., Johnston, J., Kelley, R., Obr, M., Kotecha, A. & Zhong, E. D. (2023). bioRxiv, 2023.08.18.553799.  Google Scholar
First citationReboul, C. F., Bonnet, F., Elmlund, D. & Elmlund, H. (2016). Structure, 24, 988–996.  CrossRef CAS PubMed Google Scholar
First citationRohou, A. & Grigorieff, N. (2015). J. Struct. Biol. 192, 216–221.  Web of Science CrossRef PubMed Google Scholar
First citationRoseman, A. M. (2003). Ultramicroscopy, 94, 225–236.  Web of Science CrossRef PubMed CAS Google Scholar
First citationRosenthal, P. B. & Henderson, R. (2003). J. Mol. Biol. 333, 721–745.  Web of Science CrossRef PubMed CAS Google Scholar
First citationSanchez, R. M., Zhang, Y., Chen, W., Dietrich, L. & Kudryashev, M. (2020). Nat. Commun. 11, 3709.  Web of Science CrossRef PubMed Google Scholar
First citationScheres, S. H. W. (2012). J. Struct. Biol. 180, 519–530.  Web of Science CrossRef CAS PubMed Google Scholar
First citationScheres, S. H. W. & Chen, S. (2012). Nat. Methods, 9, 853–854.  Web of Science CrossRef CAS PubMed Google Scholar
First citationSchiøtz, O. H., Kaiser, C. J. O., Klumpe, S., Morado, D. R., Poege, M., Schneider, J., Beck, F., Thompson, C. & Plitzko, M. J. (2023). Nat. Methods, https://doi.org/10.1038/s41592-023-02113-5Google Scholar
First citationSchmid, M. F. & Booth, C. R. (2008). J. Struct. Biol. 161, 243–248.  CrossRef PubMed Google Scholar
First citationSchur, F. K. (2019). Curr. Opin. Struct. Biol. 58, 1–9.  CrossRef CAS PubMed Google Scholar
First citationSorzano, C. O. S., Bilbao-Castro, J. R., Shkolnisky, Y., Alcorlo, M., Melero, R., Caffarena-Fernández, G., Li, M., Xu, G., Marabini, R. & Carazo, J. M. (2010). J. Struct. Biol. 171, 197–206.  Web of Science CrossRef CAS PubMed Google Scholar
First citationTegunov, D., Xue, L., Dienemann, C., Cramer, P. & Mahamid, J. (2021). Nat. Methods, 18, 186–193.  Web of Science CrossRef CAS PubMed Google Scholar
First citationTuroňová, B., Schur, F. K. M., Wan, W. & Briggs, J. A. G. (2017). J. Struct. Biol. 199, 187–195.  Web of Science PubMed Google Scholar
First citationTuroňová, B., Sikora, M., Schürmann, C., Hagen, W. J. H., Welsch, S., Blanc, F. E. C., von Bülow, S., Gecht, M., Bagola, K., Hörner, C., van Zandbergen, G., Landry, J., de Azevedo, N. T. D., Mosalaganti, S., Schwarz, A., Covino, R., Mühlebach, M. D., Hummer, G., Krijnse Locker, J. & Beck, M. (2020). Science, 370, 203–208.  PubMed Google Scholar
First citationWade, R. H. (1992). Ultramicroscopy, 46, 145–156.  CrossRef CAS Web of Science Google Scholar
First citationWan, W. & Briggs, J. A. G. (2016). Methods Enzymol. 579, 329–367.  Web of Science CrossRef CAS PubMed Google Scholar
First citationXing, H., Taniguchi, R., Khusainov, I., Kreysing, J. P., Welsch, S., Turoňová, B. & Beck, M. (2023). Science, 381, 70–75.  CrossRef CAS PubMed Google Scholar
First citationXiong, Q., Morphew, M. K., Schwartz, C. L., Hoenger, A. H. & Mastronarde, D. N. (2009). J. Struct. Biol. 168, 378–387.  Web of Science CrossRef PubMed Google Scholar
First citationZhang, P. (2019). Curr. Opin. Struct. Biol. 58, 249–258.  Web of Science CrossRef CAS PubMed Google Scholar
First citationZheng, S., Wolff, G., Greenan, G., Chen, Z., Faas, F. G. A., Bárcena, M., Koster, A. J., Cheng, Y. & Agard, D. A. (2022). J. Struct. Biol. X, 6, 100068.  Web of Science PubMed Google Scholar
First citationZheng, S. Q., Palovcak, E., Armache, J.-P., Verba, K. A., Cheng, Y. & Agard, D. A. (2017). Nat. Methods, 14, 331–332.  Web of Science CrossRef CAS PubMed Google Scholar
First citationZivanov, J., Nakane, T., Forsberg, B. O., Kimanius, D., Hagen, W. J., Lindahl, E. & Scheres, S. H. W. (2018). eLife, 7, e42166.  Web of Science CrossRef PubMed Google Scholar
First citationZivanov, J., Otón, J., Ke, Z., von Kügelgen, A., Pyle, E., Qu, K., Morado, D., Castaño-Díez, D., Zanetti, G., Bharat, T. A., Briggs, J. A. & Scheres, S. H. W. (2022). eLife, 11, e83724.  Web of Science CrossRef PubMed Google Scholar

留言 (0)

沒有登入
gif