InstaMap: instant-NGP for cryo-EM density maps

References

First citationArridge, S., Maass, P., Öktem, O. & Schönlieb, C.-B. (2019). Acta Numer. 28, 1–174.  Web of Science CrossRef Google Scholar
First citationAstore, M. A., Woollard, G., Silva-Sánchez, D., Zhao, W., Dao Duc, K., Grigorieff, N., Cossio, P. & Hanson, S. M. (2023). The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge. https://osf.io/8h6fz/Google Scholar
First citationBlaschke, T. (2010). ISPRS J. Photogram. Remote Sens. 65, 2–16.  Google Scholar
First citationBojarski, M., Testa, D. D., Dworakowski, D., Firner, B., Flepp, B., Goyal, P., Jackel, L. D., Monfort, M., Muller, U., Zhang, J., Zhang, X., Zhao, J. & Zieba, K. (2016). arXiv:1604.07316.  Google Scholar
First citationBreugel, F. van, Kutz, J. N. & Brunton, B. W. (2020). IEEE Access, 8, 196865–196877.  PubMed Google Scholar
First citationBronstein, M. M., Bruna, J., Cohen, T. & Veličković, P. (2021). arXiv:2104.13478.  Google Scholar
First citationBrzezinski, P. (2017). The Development of Cryo-Electron Microscopy. https://www.nobelprize.org/uploads/2018/06/advanced-chemistryprize2017.pdfGoogle Scholar
First citationChen, M. & Ludtke, S. J. (2021). Nat. Methods, 18, 930–936.  Web of Science CrossRef CAS PubMed Google Scholar
First citationChen, M., Toader, B. & Lederman, R. (2023). J. Mol. Biol. 435, 168014.  PubMed Google Scholar
First citationCheng, Z., Esteves, C., Jampani, V., Kar, A., Maji, S. & Makadia, A. (2023). arXiv:2306.05410.  Google Scholar
First citationCorso, G., El Nesr, G. & Wayment-Steele, H. K. (2024). PRX Life, 2, 040001.  Google Scholar
First citationCossio, P. & Hummer, G. (2013). J. Struct. Biol. 184, 427–437.  CAS PubMed Google Scholar
First citationCossio, P., Rohr, D., Baruffa, F., Rampp, M., Lindenstruth, V. & Hummer, G. (2017). Comput. Phys. Commun. 210, 163–171.  CAS Google Scholar
First citationDingeldein, L., Cossio, P. & Covino, R. (2024). Curr. Opin. Struct. Biol. 91, 102988.  Google Scholar
First citationDingeldein, L., Silva-Sánchez, D., Evans, L., D'Imprima, E., Grigorieff, N., Covino, R. & Cossio, P. (2024). bioRxiv, 2024.07.23.604154.  Google Scholar
First citationDonnat, C., Levy, A., Poitevin, F., Zhong, E. D. & Miolane, N. (2022). J. Struct. Biol. 214, 107920.  PubMed Google Scholar
First citationEdelberg, D. G. & Lederman, R. R. (2023). arXiv:303.07487.  Google Scholar
First citationEslami, S. M. A., Jimenez Rezende, D., Besse, F., Viola, F., Morcos, A. S., Garnelo, M., Ruderman, A., Rusu, A. A., Danihelka, I., Gregor, K., Reichert, D. P., Buesing, L., Weber, T., Vinyals, O., Rosenbaum, D., Rabinowitz, N., King, H., Hillier, C., Botvinick, M., Wierstra, D., Kavukcuoglu, K. & Hassabis, D. (2018). Science, 360, 1204–1210.  CAS PubMed Google Scholar
First citationGlaeser, R. M., Nogales, E. & Chiu, W. (2021). Editors. Single-particle Cryo-EM of Biological Macromolecules. Bristol: IOP Publishing.  Google Scholar
First citationGrant, T., Rohou, A. & Grigorieff, N. (2018). eLife, 7, e35383.  Web of Science CrossRef PubMed Google Scholar
First citationGupta, H., Phan, T. H., Yoo, J. & Unser, M. (2020). Computer Vision – ECCV 2020 Workshops, edited by A. Bartoli & A. Fusiello, pp. 429–444. Cham: Springer.  Google Scholar
First citationHeel, M. van & Harauz, G. (1986). Optik, 78, 146–156.  Google Scholar
First citationHerreros, D., Lederman, R. R., Krieger, J. M., Jiménez-Moreno, A., Martínez, M., Myška, D., Strelak, D., Filipovic, J., Sorzano, C. O. S. & Carazo, J. M. (2023). Nat Commun, 14, 154.  PubMed Google Scholar
First citationHerreros, D., Mata, C., Noddings, C., Irene, D., Krieger, J., Agard, D., Tsai, M.-D., Sorzano, C. & Carazo, J. (2024). bioRxiv, 2024.09.16.613176.  Google Scholar
First citationHimes, B. & Grigorieff, N. (2021). IUCrJ, 8, 943–953.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationHooker, S. (2021). Commun. ACM, 64, 58–65.  Google Scholar
First citationJensen, G. J. (2010). Editor. Methods in Enzymology, Vol. 482, Cryo-EM, Part B: 3-D Reconstruction. San Diego: Academic Press.  Google Scholar
First citationJeon, M., Raghu, R., Astore, M., Woollard, G., Feathers, R., Kaz, A., Hanson, S. M., Cossio, P. & Zhong, E. D. (2024). arXiv:2408.05526.  Google Scholar
First citationJumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. & Hassabis, D. (2021). Nature, 596, 583–589.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKerbl, B., Kopanas, G., Leimkuehler, T. & Drettakis, G. (2023). ACM Trans. Graph. 42, 1–14.  Google Scholar
First citationKimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. (2021). Biochem. J. 478, 4169–4185.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKimanius, D., Jamali, K. & Scheres, S. H. W. (2022). Adv. Neural Inf. Process. Syst. 35, 12395–12408  Google Scholar
First citationKimanius, D., Jamali, K., Wilkinson, M. E., Lövestam, S., Velazhahan, V., Nakane, T. & Scheres, S. H. W. (2024). Nat. Methods, 21, 1216–1221.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKimanius, D., Zickert, G., Nakane, T., Adler, J., Lunz, S., Schönlieb, C.-B., Öktem, O. & Scheres, S. H. W. (2021). IUCrJ, 8, 60–75.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationKirkland, E. J. (2020). Advanced Computing in Electron Microscopy. Cham: Springer International.  Google Scholar
First citationKleywegt, G. J., Adams, P. D., Butcher, S. J., Lawson, C. L., Rohou, A., Rosenthal, P. B., Subramaniam, S., Topf, M., Abbott, S., Baldwin, P. R., Berrisford, J. M., Bricogne, G., Choudhary, P., Croll, T. I., Danev, R., Ganesan, S. J., Grant, T., Gutmanas, A., Henderson, R., Heymann, J. B., Huiskonen, J. T., Istrate, A., Kato, T., Lander, G. C., Lok, S.-M., Ludtke, S. J., Murshudov, G. N., Pye, R., Pintilie, G. D., Richardson, J. S., Sachse, C., Salih, O., Scheres, S. H. W., Schroeder, G. F., Sorzano, C. O. S., Stagg, S. M., Wang, Z., Warshamanage, R., Westbrook, J. D., Winn, M. D., Young, J. Y., Burley, S. K., Hoch, J. C., Kurisu, G., Morris, K., Patwardhan, A. & Velankar, S. (2024). IUCrJ, 11, 140–151.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationKlindt, D. A., Hyvärinen, A., Levy, A., Miolane, N. & Poitevin, F. (2024). Front. Mol. Biosci. 11, 1393564.  PubMed Google Scholar
First citationKoo, B., Martel, J., Peck, A., Levy, A., Poitevin, F. & Miolane, N. (2023). arXiv:2306.07274.  Google Scholar
First citationKopanas, G., Philip, J., Leimkühler, T. & Drettakis, G. (2021). Comput. Graph. Forum, 40, 29–43.  Google Scholar
First citationLander, G. C. (2024). Curr. Opin. Struct. Biol. 89, 102918.  PubMed Google Scholar
First citationLavin, A., Zenil, H., Paige, B., Krakauer, D., Gottschlich, J., Mattson, T., Anandkumar, A., Choudry, S., Rocki, K., Baydin, A. G., Prunkl, C., Paige, B., Isayev, O., Peterson, E., McMahon, P. L., Macke, J., Cranmer, K., Zhang, J., Wainwright, H., Hanuka, A., Veloso, M., Assefa, S., Zheng, S. & Pfeffer, A. (2021). arXiv:2112.03235.  Google Scholar
First citationLawson, C. L., Kryshtafovych, A., Adams, P. D., Afonine, P. V., Baker, M. L., Barad, B. A., Bond, P., Burnley, T., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K., Dill, K. A., DiMaio, F., Farrell, D. P., Fraser, J. S., Herzik, M. A., Hoh, S. W., Hou, J., Hung, L.-W., Igaev, M., Joseph, A. P., Kihara, D., Kumar, D., Mittal, S., Monastyrskyy, B., Olek, M., Palmer, C. M., Patwardhan, A., Perez, A., Pfab, J., Pintilie, G. D., Richardson, J. S., Rosenthal, P. B., Sarkar, D., Schäfer, L. U., Schmid, M. F., Schröder, G. F., Shekhar, M., Si, D., Singharoy, A., Terashi, G., Terwilliger, T. C., Vaiana, A., Wang, L., Wang, Z., Wankowicz, S. A., Williams, C. J., Winn, M., Wu, T., Yu, X., Zhang, K., Berman, H. M. & Chiu, W. (2021). Nat. Methods, 18, 156–164.  Web of Science CrossRef CAS PubMed Google Scholar
First citationLawson, C. L., Kryshtafovych, A., Pintilie, G. D., Burley, S. K., Černý, J., Chen, V. B., Emsley, P., Gobbi, A., Joachimiak, A., Noreng, S., Prisant, M. G., Read, R. J., Richardson, J. S., Rohou, A. L., Schneider, B., Sellers, B. D., Shao, C., Sourial, E., Williams, C. I., Williams, C. J., Yang, Y., Abbaraju, V., Afonine, P. V., Baker, M. L., Bond, P. S., Blundell, T. L., Burnley, T., Campbell, A., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K. D., DiMaio, F., Esmaeeli, R., Giri, N., Grubmüller, H., Hoh, S. W., Hou, J., Hryc, C. F., Hunte, C., Igaev, M., Joseph, A. P., Kao, W.-C., Kihara, D., Kumar, D., Lang, L., Lin, S., Maddhuri Venkata Subramaniya, S. R., Mittal, S., Mondal, A., Moriarty, N. W., Muenks, A., Murshudov, G. N., Nicholls, R. A., Olek, M., Palmer, C. M., Perez, A., Pohjolainen, E., Pothula, K. R., Rowley, C. N., Sarkar, D., Schäfer, L. U., Schlicksup, C. J., Schröder, G. F., Shekhar, M., Si, D., Singharoy, A., Sobolev, O. V., Terashi, G., Vaiana, A. C., Vedithi, S. C., Verburgt, J., Wang, X., Warshamanage, R., Winn, M. D., Weyand, S., Yamashita, K., Zhao, M., Schmid, M. F., Berman, H. M. & Chiu, W. (2024). Nat. Methods, 21, 1340–1348.  CAS PubMed Google Scholar
First citationLevy, A., Grzadkowski, M., Poitevin, F., Vallese, F., Clarke, O. B., Wetzstein, G. & Zhong, E. D. (2024). bioRxiv, 2024.05.30.596729.  Google Scholar
First citationLevy, A., Matthews, M., Sela, M., Wetzstein, G. & Lagun, D. (2023). arXiv:2303.08096.  Google Scholar
First citationLevy, A., Poitevin, F., Martel, J., Nashed, Y., Peck, A., Miolane, N., Ratner, D., Dunne, M. & Wetzstein, G. (2022). Computer Vision – ECCV 2022, edited by S. Avidan, G. Brostow, M. Cissé, G. M. Farinella & T. Hassner, pp. 540–557. Cham: Springer Nature Switzerland.  Google Scholar
First citationLevy, A., Raghu, R., Shustin, D., Peng, A. R.-Y., Li, H., Clarke, O. B., Wetzstein, G. & Zhong, E. D. (2024). Thirty-eighth Annual Conference on Neural Information Processing Systems.  Google Scholar
First citationLevy, A., Wetzstein, G., Martel, J., Poitevin, F. & Zhong, E. D. (2022). Adv. Neural Inf. Process. Syst. 35, 13038–13049.  PubMed Google Scholar
First citationLi, H., Yu, Z., Zhao, Q., Luo, Y., Cheng, S., Zhong, T., Woo, C. M., Liu, H., Wang, L. V., Zheng, Y. & Lai, P. (2023). Photon. Res. 11, 631.  Google Scholar
First citationLi, Y., Zhou, Y., Yuan, J., Ye, F. & Gu, Q. (2024). Nat. Methods, 21, 2318–2326.  CAS PubMed Google Scholar
First citationLin, C.-H., Ma, W.-C., Torralba, A. & Lucey, S. (2021). 2021 IEEE/CVF International Conference on Computer Vision (ICCV), pp. 5741–5751. Piscataway: IEEE.  Google Scholar
First citationLobato, I. & Van Dyck, D. (2014). Acta Cryst. A70, 636–649.  Web of Science CrossRef IUCr Journals Google Scholar
First citationLu, Y., Jiang, K., Levine, J. A. & Berger, M. (2021). Comput. Graph. Forum, 40, 135–146.  Google Scholar
First citationMeng, E. C., Goddard, T. D., Pettersen, E. F., Couch, G. S., Pearson, Z. J., Morris, J. H. & Ferrin, T. E. (2023). Protein Sci. 32, e4792.  Web of Science CrossRef PubMed Google Scholar
First citationMeng, Q., Chen, A., Luo, H., Wu, M., Su, H., Xu, L., He, X. & Yu, J. (2021). 2021 IEEE/CVF International Conference on Computer Vision (ICCV), pp. 6351–6361. Piscataway: IEEE.  Google Scholar
First citationMildenhall, B., Srinivasan, P. P., Tancik, M., Barron, J. T., Ramamoorthi, R. & Ng, R. (2020). Computer Vision – ECCV 2020 Workshops, edited by A. Bartoli & A. Fusiello, pp. 405–421. Cham: Springer.  Google Scholar
First citationMildenhall, B., Srinivasan, P. P., Tancik, M., Barron, J. T., Ramamoorthi, R. & Ng, R. (2022). Commun. ACM, 65, 99–106.  Google Scholar
First citationMukherjee, S., Carioni, M., Öktem, O. & Schönlieb, C.-B. (2021). NIPS'21: Proceedings of the 35th International Conference on Neural Information Processing Systems, pp. 21413–21425. Red Hook: Curran Associates.  Google Scholar
First citationMüller, T., Evans, A., Schied, C. & Keller, A. (2022). ACM Trans. Graph. 41, 102.  Google Scholar
First citationMüller, T., Mcwilliams, B., Rousselle, F., Gross, M. & Novák, J. (2019). ACM Trans. Graph. 38, 145.  Google Scholar
First citationMüller, T., Rousselle, F., Keller, A. & Novák, J. (2020). ACM Trans. Graph. 39, 243.  Google Scholar
First citationMüller, T., Rousselle, F., Novák, J. & Keller, A. (2021). ACM Trans. Graph. 40, 36.  Google Scholar
First citationNashed, Y., Peck, A., Martel, J., Levy, A., Koo, B., Wetzstein, G., Miolane, N., Ratner, D. & Poitevin, F. (2022). arXiv:2209.15121.  Google Scholar
First citationNashed, Y. S. G., Poitevin, F., Gupta, H., Woollard, G., Kagan, M., Yoon, C. H. & Ratner, D. (2021). 2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), pp. 4049–4059. Piscataway: IEEE.  Google Scholar
First citationNguyen, N., Liang, F., Engel, D., Bohak, C., Strnad, O., Ropinski, T. & Viola, I. (2024). 2024 IEEE 17th Pacific Visualization Conference (PacificVis), pp. 62–71. Piscataway: IEEE.  Google Scholar
First citationOngie, G., Jalal, A., Metzler, C. A., Baraniuk, R. G., Dimakis, A. G. & Willett, R. (2020). IEEE J. Sel. Areas Inf. Theory, 1, 39–56.  Google Scholar
First citationPapillon, M., Sanborn, S., Hajij, M. & Miolane, N. (2023). arXiv:2304.10031.  Google Scholar
First citationPark, K., Sinha, U., Hedman, P., Barron, J. T., Bouaziz, S., Goldman, D. B., Martin-Brualla, R. & Seitz, S. M. (2021). ACM Trans. Graph. 40, 238.  Google Scholar
First citationParkhurst, J. M., Dumoux, M., Basham, M., Clare, D., Siebert, C. A., Varslot, T., Kirkland, A., Naismith, J. H. & Evans, G. (2021). Open Biol. 11, 210160.  Web of Science CrossRef PubMed Google Scholar
First citationPenczek, P. A. (2010). Methods Enzymol. 482, 73–100.  Web of Science CrossRef CAS PubMed Google Scholar
First citationPetitjean, A., Poirier-Ginter, Y., Tewari, A., Cordonnier, G. & Drettakis, G. (2023). Comput. Graph. Forum, 42, e14888. 

Comments (0)

No login
gif