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.  Web of Science 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.  Web of Science 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.  Web of Science 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.  Web of Science 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.  Web of Science 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.  Web of Science 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.  Web of Science 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.  Web of Science CrossRef PubMed Google Scholar
First citationMilicevic, N., Jenner, L., Myasnikov, A., Yusupov, M. & Yusupova, G. (2024). Nature, 625, 393–400.  Web of Science 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.  Web of Science 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.  Web of Science 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.  Web of Science CrossRef PubMed Google Scholar
First citationSchur, F. K. (2019). Curr. Opin. Struct. Biol. 58, 1–9.  Web of Science 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.  Web of Science 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.  Web of Science 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

Comments (0)

No login
gif