The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Abstract
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Model geometries were assessed using the MolProbity module in Phenix, the Molprobity server, and the PDB Validation server.
“Model geometries were assessed using the MolProbity module in Phenix, the Molprobity server68 (http://molprobity.biochem.duke.edu/), and the PDB Validation server69 (www.wwpdb.org).”
From Structural organization of the retriever–CCC endosomal recycling complex (2024) · cites this paper as [69]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Matplotlib: a 2D graphics environment
Hunter, J. D. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.55 · Cited by 39,249
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
Self-citationTowards automated crystallographic structure refinement with phenix.refine
Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H., & Adams, P. D. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444912001308 · Cited by 5,511
Self-citationKühlbrandt, W. (2014) · Science · doi:10.1126/science.1251652 · Cited by 1,325
De novo modeling in cryo-EM density maps with Pathwalking
Chen, M., Baldwin, P. R., Ludtke, S. J., & Baker, M. L. (2016) · Journal of Structural Biology · doi:10.1016/j.jsb.2016.06.004 · Cited by 82
Flagged first, then by citations
Research works printed but not linked: 151
- Abrahams, 2003, C/C++ Users J., 21, 29
- Adams, 2019, Acta Cryst. D, 75, 451, 10.1107/S2059798319004522 · DOI
- Adams, 2010, Acta Cryst. D, 66, 213, 10.1107/S0907444909052925 · DOI · Paper page
- Adams, 2009, Curr. Opin. Struct. Biol., 19, 566, 10.1016/j.sbi.2009.07.014 · DOI
- Adams, 2002, Acta Cryst. D, 58, 1948, 10.1107/S0907444902016657 · DOI · Paper page
- Adams, 2009, Acta Cryst. D, 65, 567, 10.1107/S0907444909011548 · DOI
- Afonine, 2018, Acta Cryst. D, 74, 621, 10.1107/S2059798318005764 · DOI
- Afonine, 2005, Acta Cryst. D, 61, 850, 10.1107/S0907444905007894 · DOI
- Afonine, 2007, Acta Cryst. D, 63, 1194, 10.1107/S0907444907046148 · DOI
- Afonine, 2013, Acta Cryst. D, 69, 625, 10.1107/S0907444913000462 · DOI
- Afonine, 2009, J. Appl. Cryst., 42, 607, 10.1107/S0021889809023528 · DOI
- Afonine, 2018, Acta Cryst. D, 74, 814, 10.1107/S2059798318009324 · DOI
- Afonine, 2015, Acta Cryst. D, 71, 646, 10.1107/S1399004714028132 · DOI
- Afonine, 2010, Acta Cryst. D, 66, 1153, 10.1107/S0907444910026582 · DOI
- Afonine, 2018, Acta Cryst. D, 74, 531, 10.1107/S2059798318006551 · DOI
- Bai, 2015, Trends Biochem. Sci., 40, 49, 10.1016/j.tibs.2014.10.005 · DOI
- Baker, 2012, Structure, 20, 450, 10.1016/j.str.2012.01.008 · DOI
- Barad, 2015, Nature Methods, 12, 943, 10.1038/nmeth.3541 · DOI · Paper page
- Berkholz, 2009, Structure, 17, 1316, 10.1016/j.str.2009.08.012 · DOI
- Bernstein, 1977, J. Mol. Biol., 112, 535, 10.1016/S0022-2836(77)80200-3 · DOI
- Blow, D. M., Navaza, J., Tong, L., Arnold, E. & Rossmann, M. G. (2012). International Tables for Crystallography, Vol. F, edited by E. Arnold, D. M. Himmel & M. G. Rossmann, pp. 333-366. Chichester: John Wiley & Sons.
- Borbulevych, 2014, Comput. Crystallogr. Newsl., 5, 26
- Brändén, 1990, Nature (London), 343, 687, 10.1038/343687a0 · DOI
- Britton, 1972, Acta Cryst. A, 28, 296, 10.1107/S0567739472000786 · DOI
- Brünger, 1992, Nature (London), 355, 472, 10.1038/355472a0 · DOI
- Brünger, 1998, Acta Cryst. D, 54, 905, 10.1107/S0907444998003254 · DOI
- Brunger, 2012, Acta Cryst. D, 68, 391, 10.1107/S090744491104978X · DOI
- Bryan, 2013, Acta Cryst. F, 69, 1015, 10.1107/S1744309113021386 · DOI
- Bunkóczi, 2013, Acta Cryst. D, 69, 2276, 10.1107/S0907444913022750 · DOI
- Bunkóczi, 2011, Acta Cryst. D, 67, 303, 10.1107/S0907444910051218 · DOI
- Burley, 2019, Nucleic Acids Res., 47, D464, 10.1093/nar/gky1004 · DOI
- Burnley, 2012, Elife, 1, e00311, 10.7554/eLife.00311 · DOI
- Busing, 1964, Acta Cryst., 17, 142, 10.1107/S0365110X64000408 · DOI
- Cardone, 2013, J. Struct. Biol., 184, 226, 10.1016/j.jsb.2013.08.002 · DOI
- Chapman, 2011, Nature (London), 470, 73, 10.1038/nature09750 · DOI
- Chen, 2010, Acta Cryst. D, 66, 12, 10.1107/S0907444909042073 · DOI · Paper page
- Chen, 2009, Protein Sci., 18, 2403, 10.1002/pro.250 · DOI
- Chou, 2013, Nature Methods, 10, 74, 10.1038/nmeth.2262 · DOI
- Clowney, 1996, J. Am. Chem. Soc., 118, 509, 10.1021/ja952883d · DOI
- Coppens, 1967, Science, 158, 1577, 10.1126/science.158.3808.1577 · DOI
- Croll, 2015, Acta Cryst. D, 71, 706, 10.1107/S1399004715000826 · DOI
- Croll, 2018, Acta Cryst. D, 74, 519, 10.1107/S2059798318002425 · DOI
- Dauter, 2017, Methods Mol. Biol., 1607, 349, 10.1007/978-1-4939-7000-1_14 · DOI
- Deis, 2013, Comput. Crystallogr. Newsl., 4, 9
- Diederichs, 2017, Methods Mol. Biol., 1607, 239, 10.1007/978-1-4939-7000-1_10 · DOI
- DiMaio, 2013, Nature Methods, 10, 1102, 10.1038/nmeth.2648 · DOI
- DiMaio, 2011, Nature (London), 473, 540, 10.1038/nature09964 · DOI
- Emsley, 2010, Acta Cryst. D, 66, 486, 10.1107/S0907444910007493 · DOI · Paper page
- Engh, 1991, Acta Cryst. A, 47, 392, 10.1107/S0108767391001071 · DOI
- Evans, 2007, Acta Cryst. D, 63, 58, 10.1107/S090744490604604X · DOI
- Evans, 2008, Acta Cryst. D, 64, 1, 10.1107/S0907444907051554 · DOI
- Fernández, 2008, J. Struct. Biol., 164, 170, 10.1016/j.jsb.2008.05.010 · DOI
- Gelbin, 1996, J. Am. Chem. Soc., 118, 519, 10.1021/ja9528846 · DOI
- Goddard, 2018, Protein Sci., 27, 14, 10.1002/pro.3235 · DOI · Paper page
- Grosse-Kunstleve, 2003, Acta Cryst. D, 59, 1966, 10.1107/S0907444903018043 · DOI
- Grosse-Kunstleve, R. W., Moriarty, N. W. & Adams, P. D. (2009). Proceedings of the ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, Vol. 4, pp. 1477-1485. New York: ASME.
- Grosse-Kunstleve, 2002, J. Appl. Cryst., 35, 126, 10.1107/S0021889801017824 · DOI
- Gruene, 2018, Angew. Chem. Int. Ed., 57, 16313, 10.1002/anie.201811318 · DOI
- Hahn, T. & Klapper, H. (2006). International Tables for Crystallography, Vol. D, edited by A. Authier, pp. 393-448. Dordrecht: Kluwer.
- Headd, 2012, Acta Cryst. D, 68, 381, 10.1107/S0907444911047834 · DOI
- Headd, 2014, Acta Cryst. D, 70, 1346, 10.1107/S1399004714003277 · DOI
- Heel, 1986, Optik, 73, 119
- Hintze, 2016, Proteins, 84, 1177, 10.1002/prot.25039 · DOI
- Hoppe, 1957, Acta Cryst., 10, 750
- Howells, 1950, Acta Cryst., 3, 210, 10.1107/S0365110X50000513 · DOI
- Jain, 2015, Methods Enzymol., 558, 181, 10.1016/bs.mie.2015.01.007 · DOI
- Jensen, 2010, Methods Enzymol., 483, xv, 10.1016/S0076-6879(10)83021-6 · DOI
- Jones, 2018, ACS Cent. Sci., 4, 1587, 10.1021/acscentsci.8b00760 · DOI
- Jones, 1991, Acta Cryst. A, 47, 110, 10.1107/S0108767390010224 · DOI
- Kendrew, 1958, Nature (London), 181, 662, 10.1038/181662a0 · DOI
- Kim, D. N., Moriarty, N. W., Kirmizialtin, S., Afonine, P. V., Poon, B. K., Sobolev, O. V., Adams, P. D. & Sanbonmatsu, K. Y. (2019). In the press.
- Kirmizialtin, 2015, Methods Enzymol., 558, 497, 10.1016/bs.mie.2015.02.011 · DOI
- Klei, 2014, Acta Cryst. D, 70, 134, 10.1107/S1399004713030071 · DOI
- Kleywegt, 1996, Structure, 4, 897, 10.1016/S0969-2126(96)00097-4 · DOI
- Kleywegt, 1995, Structure, 3, 535, 10.1016/S0969-2126(01)00187-3 · DOI
- Knihtila, 2015, J. Biol. Chem., 290, 31025, 10.1074/jbc.M115.679860 · DOI
- Kucukelbir, 2014, Nature Methods, 11, 63, 10.1038/nmeth.2727 · DOI
- Li, 2013, Nature Methods, 10, 584, 10.1038/nmeth.2472 · DOI
- Liebschner, 2018, Acta Cryst. D, 74, 800, 10.1107/S2059798318004588 · DOI
- Liebschner, 2017, Acta Cryst. D, 73, 148, 10.1107/S2059798316018210 · DOI
- Liu, 2017, Protein Sci., 26, 8, 10.1002/pro.2989 · DOI
- Loeffelholz, 2017, Curr. Opin. Struct. Biol., 46, 140, 10.1016/j.sbi.2017.07.007 · DOI
- Lovell, 2003, Proteins, 50, 437, 10.1002/prot.10286 · DOI · Paper page
- Lutz, M. & Ascher, D. (1999). Learning Python. Sebastopol: O'Reilly Media.
- McPherson, A. (2009). Introduction to Macromolecular Crystallography. Hoboken: Wiley-Blackwell. · DOI
- Moriarty, 2019, Acta Cryst. D, 75, 16, 10.1107/S205979831801519X · DOI
- Moriarty, 2017, Acta Cryst. D, 73, 123, 10.1107/S2059798316016570 · DOI
- Moriarty, 2009, Acta Cryst. D, 65, 1074, 10.1107/S0907444909029436 · DOI
- Moriarty, 2018, Protein Sci., 27, 182, 10.1002/pro.3296 · DOI
- Moriarty, 2014, FEBS J., 281, 4061, 10.1111/febs.12860 · DOI
- Moriarty, 2016, Acta Cryst. D, 72, 176, 10.1107/S2059798315022408 · DOI
- Nannenga, 2018, Emerg. Top. Life Sci., 2, 1, 10.1042/ETLS20170082 · DOI
- Natchiar, 2017, Nature (London), 551, 472, 10.1038/nature24482 · DOI
- Oeffner, 2018, Acta Cryst. D, 74, 245, 10.1107/S2059798318004357 · DOI
- Oldfield, 2001, Acta Cryst. D, 57, 82, 10.1107/S0907444900014098 · DOI
- Orpen, 1978, Acta Cryst. B, 34, 2466, 10.1107/S0567740878014697 · DOI
- Padilla, 2003, Acta Cryst. D, 59, 1124, 10.1107/S0907444903007947 · DOI
- Penczek, 2010, Methods Enzymol., 482, 73, 10.1016/S0076-6879(10)82003-8 · DOI
- Perutz, 1960, Nature (London), 185, 416, 10.1038/185416a0 · DOI
- Podjarny, 1996, Methods Mol. Biol., 56, 205
- Popov, 2003, Acta Cryst. D, 59, 1145, 10.1107/S0907444903008163 · DOI
- Read, 2011, Structure, 19, 1395, 10.1016/j.str.2011.08.006 · DOI
- Richardson, 2015, Comput. Crystallogr. Newsl., 6, 47
- Richardson J S Schneider B Murray L W Kapral G J Immormino R M Headd J J Richardson D C Ham D Hershkovits E Williams L D Keating K S Pyle A M Micallef D Westbrook J Berman H M & RNA Ontology Consortium, 2008, RNA, 14, 465, 10.1261/rna.657708 · DOI
- Richardson, 2018, Acta Cryst. D, 74, 132, 10.1107/S2059798317009834 · DOI
- Richardson, 2018, J. Struct. Biol., 204, 301, 10.1016/j.jsb.2018.08.007 · DOI
- Roseman, 2000, Acta Cryst. D, 56, 1332, 10.1107/S0907444900010908 · DOI
- Rosenthal, 2003, J. Mol. Biol., 333, 721, 10.1016/j.jmb.2003.07.013 · DOI · Paper page
- Rossmann, 2014, IUCrJ, 1, 84, 10.1107/S2052252514000499 · DOI
- Rotkiewicz, 2008, J. Comput. Chem., 29, 1460, 10.1002/jcc.20906 · DOI
- Schlichting, 2015, IUCrJ, 2, 246, 10.1107/S205225251402702X · DOI
- Schomaker, 1968, Acta Cryst. B, 24, 63, 10.1107/S0567740868001718 · DOI
- Sheldrick, 2008, Acta Cryst. A, 64, 112, 10.1107/S0108767307043930 · DOI
- Sheldrick, 1997, Methods Enzymol., 277, 319, 10.1016/S0076-6879(97)77018-6 · DOI
- Sobolev, 2015, J. Appl. Cryst., 48, 1130, 10.1107/S1600576715010432 · DOI
- Standfuss, 2017, IUCrJ, 4, 100, 10.1107/S2052252517001877 · DOI
- Taylor, 2010, Acta Cryst. D, 66, 325, 10.1107/S0907444910006694 · DOI
- Terwilliger, 2000, Acta Cryst. D, 56, 965, 10.1107/S0907444900005072 · DOI
- Terwilliger, 2002, Acta Cryst. D, 58, 1937, 10.1107/S0907444902016438 · DOI
- Terwilliger, 2018, Comput. Crystallogr. Newsl., 9, 51
- Terwilliger, 2018, Nature Methods, 15, 905, 10.1038/s41592-018-0173-1 · DOI
- Terwilliger, 2007, Acta Cryst. D, 63, 101, 10.1107/S0907444906046233 · DOI
- Terwilliger, 2009, Acta Cryst. D, 65, 582, 10.1107/S0907444909012098 · DOI
- Terwilliger, 1999, Acta Cryst. D, 55, 849, 10.1107/S0907444999000839 · DOI
- Terwilliger, 2016, Acta Cryst. D, 72, 346, 10.1107/S2059798315019269 · DOI
- Terwilliger, 2016, Acta Cryst. D, 72, 359, 10.1107/S2059798315019403 · DOI
- Terwilliger, 2012, J. Struct. Funct. Genomics, 13, 81, 10.1007/s10969-012-9129-3 · DOI
- Terwilliger, 2008, Acta Cryst. D, 64, 61, 10.1107/S090744490705024X · DOI · Paper page
- Terwilliger, 2006, Acta Cryst. D, 62, 915, 10.1107/S0907444906017161 · DOI
- Terwilliger, 2013, Acta Cryst. D, 69, 2244, 10.1107/S0907444913017770 · DOI
- Terwilliger, 2018, Acta Cryst. D, 74, 545, 10.1107/S2059798318004655 · DOI
- Urzhumtsev, 2014, Acta Cryst. D, 70, 2593, 10.1107/S1399004714016289 · DOI
- Urzhumtsev, 2016, Acta Cryst. D, 72, 1073, 10.1107/S2059798316013048 · DOI
- Urzhumtseva, 2009, Acta Cryst. D, 65, 297, 10.1107/S0907444908044296 · DOI · Paper page
- Vagin, 2004, IUCr Comput. Comm. Newsl., 4, 59
- Vagin, 2004, Acta Cryst. D, 60, 2184, 10.1107/S0907444904023510 · DOI
- Wall, 2014, Structure, 22, 182, 10.1016/j.str.2014.01.002 · DOI
- Wall, 2018, Curr. Opin. Struct. Biol., 50, 109, 10.1016/j.sbi.2018.01.009 · DOI
- Wang, 2017, Protein Sci., 26, 122, 10.1002/pro.3060 · DOI
- Williams, 2018, Protein Sci., 27, 293, 10.1002/pro.3330 · DOI · Paper page
- Williams, 2018, BioRxiv, 324517
- Wlodawer, 1980, Acta Cryst. B, 36, 1826, 10.1107/S0567740880007315 · DOI
- Wlodawer, 1982, Acta Cryst. A, 38, 239, 10.1107/S0567739482000527 · DOI
- Wlodawer, 2013, FEBS J., 280, 5705, 10.1111/febs.12495 · DOI
- Word, 1999, J. Mol. Biol., 285, 1711, 10.1006/jmbi.1998.2400 · DOI
- Word, 1999, J. Mol. Biol., 285, 1735, 10.1006/jmbi.1998.2401 · DOI
- Yamaguchi, 2009, Proc. Natl. Acad. Sci. USA, 106, 440, 10.1073/pnas.0811882106 · DOI
- Yeates, 1997, Methods Enzymol., 276, 344, 10.1016/S0076-6879(97)76068-3 · DOI
- Zheng, 2017, Acta Cryst. D, 73, 1020, 10.1107/S2059798317016746 · DOI
- Zheng, 2017, Acta Cryst. D, 73, 45, 10.1107/S2059798316019847 · DOI
- Zwart, 2005, Acta Cryst. D, 61, 1437, 10.1107/S0907444905023589 · DOI
Cited by
Sorted by citations
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586
Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549
Self-citationStructural basis of receptor recognition by SARS-CoV-2
Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020) · Nature · doi:10.1038/s41586-020-2179-y · Cited by 3,661
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody
Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2349-y · Cited by 1,885
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes
Hsieh, C.-L., Goldsmith, J. A., Schaub, J. M., DiVenere, A. M., Kuo, H.-C., Javanmardi, K., Le, K. C., Wrapp, D., Lee, A. G., Liu, Y., et al. (2020) · Science · doi:10.1126/science.abd0826 · Cited by 1,303
Cao, Y., Su, B., Guo, X., Sun, W., Deng, Y., Bao, L., Zhu, Q., Zhang, X., Zheng, Y., Geng, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.025 · Cited by 1,188
N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.028 · Cited by 901
“, 2016), Phenix (Liebschner et al., 2019) and ISOLDE (Croll, 2018).”
SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses
Dejnirattisai, W., Huo, J., Zhou, D., Zahradník, J., Supasa, P., Liu, C., Duyvesteyn, H. M. E., Ginn, H. M., Mentzer, A. J., Tuekprakhon, A., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.046 · Cited by 930
Self-citationA structural biology community assessment of AlphaFold2 applications
Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00849-w · Cited by 675
Self-citationReduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum
Liu, C., Ginn, H. M., Dejnirattisai, W., Supasa, P., Wang, B., Tuekprakhon, A., Nutalai, R., Zhou, D., Mentzer, A. J., Zhao, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.020 · Cited by 669
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
Cao, L., Goreshnik, I., Coventry, B., Case, J. B., Miller, L., Kozodoy, L., Chen, R. E., Carter, L., Walls, A. C., Park, Y.-J., et al. (2020) · Science · doi:10.1126/science.abd9909 · Cited by 742
SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex
Mannar, D., Saville, J. W., Zhu, X., Srivastava, S. S., Berezuk, A. M., Tuttle, K. S., Marquez, A. C., Sekirov, I., & Subramaniam, S. (2022) · Science · doi:10.1126/science.abn7760 · Cited by 630
Automated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686
Antibody evasion by the P.1 strain of SARS-CoV-2
Dejnirattisai, W., Zhou, D., Supasa, P., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Tuekprakhon, A., Nutalai, R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.055 · Cited by 583
Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms
Tortorici, M. A., Beltramello, M., Lempp, F. A., Pinto, D., Dang, H. V., Rosen, L. E., McCallum, M., Bowen, J., Minola, A., Jaconi, S., et al. (2020) · Science · doi:10.1126/science.abe3354 · Cited by 510
De novo protein design by deep network hallucination
Anishchenko, I., Chidyausiku, T. M., Ovchinnikov, S., Pellock, S. J., & Baker, D. (2020) · doi:10.1101/2020.07.22.211482 · Cited by 629
Design of protein-binding proteins from the target structure alone
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature · doi:10.1038/s41586-022-04654-9 · Cited by 577
Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
McCallum, M., Czudnochowski, N., Rosen, L. E., Zepeda, S. K., Bowen, J. E., Walls, A. C., Hauser, K., Joshi, A., Stewart, C., Dillen, J. R., et al. (2022) · Science · doi:10.1126/science.abn8652 · Cited by 535
Self-citationSARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
McCallum, M., Bassi, J., De Marco, A., Chen, A., Walls, A. C., Di Iulio, J., Tortorici, M. A., Navarro, M.-J., Silacci-Fregni, C., Saliba, C., et al. (2021) · Science · doi:10.1126/science.abi7994 · Cited by 412
Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera
Supasa, P., Zhou, D., Dejnirattisai, W., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Nutalai, R., Tuekprakhon, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.033 · Cited by 460
The antigenic anatomy of SARS-CoV-2 receptor binding domain
Dejnirattisai, W., Zhou, D., Ginn, H. M., Duyvesteyn, H. M. E., Supasa, P., Case, J. B., Zhao, Y., Walter, T. S., Mentzer, A. J., Liu, C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.032 · Cited by 371
Structure, lipid scrambling activity and role in autophagosome formation of ATG9A
Maeda, S., Yamamoto, H., Kinch, L. N., Garza, C. M., Takahashi, S., Otomo, C., Grishin, N. V., Forli, S., Mizushima, N., & Otomo, T. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-00520-2 · Cited by 305
De novo design of modular and tunable protein biosensors
Quijano-Rubio, A., Yeh, H.-W., Park, J., Lee, H., Langan, R. A., Boyken, S. E., Lajoie, M. J., Cao, L., Chow, C. M., Miranda, M. C., et al. (2021) · Nature · doi:10.1038/s41586-021-03258-z · Cited by 260
Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient
Zhou, D., Duyvesteyn, H. M. E., Chen, C.-P., Huang, C.-G., Chen, T.-H., Shih, S.-R., Lin, Y.-C., Cheng, C.-Y., Cheng, S.-H., Huang, Y.-C., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0480-y · Cited by 274
Structure of the bacterial ribosome at 2 Å resolution
Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263
Chemical remodeling of a cellular chaperone to target the active state of mutant KRAS
Schulze, C. J., Seamon, K. J., Zhao, Y., Yang, Y. C., Cregg, J., Kim, D., Tomlinson, A., Choy, T. J., Wang, Z., Sang, B., et al. (2023) · Science · doi:10.1126/science.adg9652 · Cited by 264
The molecular basis of tight nuclear tethering and inactivation of cGAS
Zhao, B., Xu, P., Rowlett, C. M., Jing, T., Shinde, O., Lei, Y., West, A. P., Liu, W. R., & Li, P. (2020) · Nature · doi:10.1038/s41586-020-2749-z · Cited by 261
Structural basis for the inhibition of cGAS by nucleosomes
Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., & Kurumizaka, H. (2020) · Science · doi:10.1126/science.abd0237 · Cited by 243
Copin, R., Baum, A., Wloga, E., Pascal, K. E., Giordano, S., Fulton, B. O., Zhou, A., Negron, N., Lanza, K., Chan, N., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.002 · Cited by 212
Computational design of serine hydrolases
Lauko, A., Pellock, S. J., Sumida, K. H., Anishchenko, I., Juergens, D., Ahern, W., Jeung, J., Shida, A. F., Hunt, A., Kalvet, I., et al. (2025) · Science · doi:10.1126/science.adu2454 · Cited by 235
Targeted protein degradation via intramolecular bivalent glues
Hsia, O., Hinterndorfer, M., Cowan, A. D., Iso, K., Ishida, T., Sundaramoorthy, R., Nakasone, M. A., Imrichova, H., Schätz, C., Rukavina, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07089-6 · Cited by 222
Structures of the σ2 receptor enable docking for bioactive ligand discovery
Alon, A., Lyu, J., Braz, J. M., Tummino, T. A., Craik, V., O’Meara, M. J., Webb, C. M., Radchenko, D. S., Moroz, Y. S., Huang, X.-P., et al. (2021) · Nature · doi:10.1038/s41586-021-04175-x · Cited by 211
Foley, M. H., Walker, M. E., Stewart, A. K., O’Flaherty, S., Gentry, E. C., Patel, S., Beaty, V. V., Allen, G., Pan, M., Simpson, J. B., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01337-7 · Cited by 181
Glassman, C. R., Mathiharan, Y. K., Jude, K. M., Su, L., Panova, O., Lupardus, P. J., Spangler, J. B., Ely, L. K., Thomas, C., Skiniotis, G., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.018 · Cited by 181
Targeting cancer with small-molecule pan-KRAS degraders
Popow, J., Farnaby, W., Gollner, A., Kofink, C., Fischer, G., Wurm, M., Zollman, D., Wijaya, A., Mischerikow, N., Hasenoehrl, C., et al. (2024) · Science · doi:10.1126/science.adm8684 · Cited by 198
Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol
Zhang, L., Zhao, Y., Gao, Y., Wu, L., Gao, R., Zhang, Q., Wang, Y., Wu, C., Wu, F., Gurcha, S. S., et al. (2020) · Science · doi:10.1126/science.aba9102 · Cited by 173
Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy
Bonazzi, S., d’Hennezel, E., Beckwith, R. E. J., Xu, L., Fazal, A., Magracheva, A., Ramesh, R., Cernijenko, A., Antonakos, B., Bhang, H.-E. C., et al. (2023) · Cell Chemical Biology · doi:10.1016/j.chembiol.2023.02.005 · Cited by 167
Cryo-EM structure of the human cardiac myosin filament
Dutta, D., Nguyen, V., Campbell, K. S., Padrón, R., & Craig, R. (2023) · Nature · doi:10.1038/s41586-023-06691-4 · Cited by 164
Structure of Human ATG9A, the Only Transmembrane Protein of the Core Autophagy Machinery
Guardia, C. M., Tan, X.-F., Lian, T., Rana, M. S., Zhou, W., Christenson, E. T., Lowry, A. J., Faraldo-Gómez, J. D., Bonifacino, J. S., Jiang, J., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107837 · Cited by 163
Assessment of three‐dimensional RNA structure prediction in CASP15
Das, R., Kretsch, R. C., Simpkin, A. J., Mulvaney, T., Pham, P., Rangan, R., Bu, F., Keegan, R. M., Topf, M., Rigden, D. J., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26602 · Cited by 139
An atlas of protein homo-oligomerization across domains of life
Schweke, H., Pacesa, M., Levin, T., Goverde, C. A., Kumar, P., Duhoo, Y., Dornfeld, L. J., Dubreuil, B., Georgeon, S., Ovchinnikov, S., et al. (2024) · Cell · doi:10.1016/j.cell.2024.01.022 · Cited by 144
A structural biology community assessment of AlphaFold 2 applications
Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · doi:10.1101/2021.09.26.461876 · Cited by 122
Self-citationDefining molecular glues with a dual-nanobody cannabidiol sensor
Cao, S., Kang, S., Mao, H., Yao, J., Gu, L., & Zheng, N. (2022) · Nature Communications · doi:10.1038/s41467-022-28507-1 · Cited by 125
Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex
Gruszczyk, J., Grandvuillemin, L., Lai-Kee-Him, J., Paloni, M., Savva, C. G., Germain, P., Grimaldi, M., Boulahtouf, A., Kwong, H.-S., Bous, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34773-w · Cited by 137
Structural basis of Gabija anti-phage defence and viral immune evasion
Antine, S. P., Johnson, A. G., Mooney, S. E., Leavitt, A., Mayer, M. L., Yirmiya, E., Amitai, G., Sorek, R., & Kranzusch, P. J. (2024) · Nature · doi:10.1038/s41586-023-06855-2 · Cited by 125
Turnbull, R. E., Fairall, L., Saleh, A., Kelsall, E., Morris, K. L., Ragan, T. J., Savva, C. G., Chandru, A., Millard, C. J., Makarova, O. V., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17078-8 · Cited by 108
A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction
Ting, P. Y., Borikar, S., Kerrigan, J. R., Thomsen, N. M., Aghania, E., Hinman, A. E., Reyes, A., Pizzato, N., Fodor, B. D., Wu, F., et al. (2024) · Science · doi:10.1126/science.adk6129 · Cited by 97
Mining the CRBN target space redefines rules for molecular glue-induced neosubstrate recognition
Petzold, G., Gainza, P., Annunziato, S., Lamberto, I., Trenh, P., McAllister, L. A., DeMarco, B., Schwander, L., Bunker, R. D., Zlotosch, M., et al. (2025) · Science · doi:10.1126/science.adt6736 · Cited by 117
Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients
Miller-Vedam, L. E., Bräuning, B., Popova, K. D., Schirle Oakdale, N. T., Bonnar, J. L., Prabu, J. R., Boydston, E. A., Sevillano, N., Shurtleff, M. J., Stroud, R. M., et al. (2020) · eLife · doi:10.7554/elife.62611 · Cited by 87
Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase
Garvie, C. W., Wu, X., Papanastasiou, M., Lee, S., Fuller, J., Schnitzler, G. R., Horner, S. W., Baker, A., Zhang, T., Mullahoo, J. P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24495-w · Cited by 85
How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication
Jones, M. L., Aria, V., Baris, Y., & Yeeles, J. T. P. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.035 · Cited by 86
Lee, K., Thwin, A. C., Nadel, C. M., Tse, E., Gates, S. N., Gestwicki, J. E., & Southworth, D. R. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.023 · Cited by 76
Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G., Bouhaddou, M., Fossati, A., Brilot, A. F., et al. (2021) · doi:10.1101/2021.05.10.443524 · Cited by 89
Pony, P., Rapisarda, C., Terradot, L., Marza, E., & Fronzes, R. (2020) · Nature Communications · doi:10.1038/s41467-020-15214-y · Cited by 82
Structure of human PINK1 at a mitochondrial TOM-VDAC array
Callegari, S., Kirk, N. S., Gan, Z. Y., Dite, T., Cobbold, S. A., Leis, A., Dagley, L. F., Glukhova, A., & Komander, D. (2025) · Science · doi:10.1126/science.adu6445 · Cited by 75
Giri, N., Roy, R. S., & Cheng, J. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102536 · Cited by 59
Structure of an endogenous mycobacterial MCE lipid transporter
Chen, J., Fruhauf, A., Fan, C., Ponce, J., Ueberheide, B., Bhabha, G., & Ekiert, D. C. (2023) · Nature · doi:10.1038/s41586-023-06366-0 · Cited by 69
Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target
Adams, O., Deme, J. C., Parker, J. L., Fowler, P. W., Lea, S. M., & Newstead, S. (2021) · Structure · doi:10.1016/j.str.2021.06.013 · Cited by 63
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE
Oeffner, R. D., Croll, T. I., Millán, C., Poon, B. K., Schlicksup, C. J., Read, R. J., & Terwilliger, T. C. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322010026 · Cited by 63
Self-citationAccelerating crystal structure determination with iterative AlphaFold prediction
Terwilliger, T. C., Afonine, P. V., Liebschner, D., Croll, T. I., McCoy, A. J., Oeffner, R. D., Williams, C. J., Poon, B. K., Richardson, J. S., Read, R. J., et al. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s205979832300102x · Cited by 62
Self-citationAster-dependent nonvesicular transport facilitates dietary cholesterol uptake
Ferrari, A., Whang, E., Xiao, X., Kennelly, J. P., Romartinez-Alonso, B., Mack, J. J., Weston, T., Chen, K., Kim, Y., Tol, M. J., et al. (2023) · Science · doi:10.1126/science.adf0966 · Cited by 61
Assessing the utility of CASP14 models for molecular replacement
Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26214 · Cited by 62
Self-citationHigh-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles
Coupland, C. E., Karimi, R., Bueler, S. A., Liang, Y., Courbon, G. M., Di Trani, J. M., Wong, C. J., Saghian, R., Youn, J.-Y., Wang, L.-Y., et al. (2024) · Science · doi:10.1126/science.adp5577 · Cited by 58
Structural insights into the assembly of gp130 family cytokine signaling complexes
Zhou, Y., Stevis, P. E., Cao, J., Saotome, K., Wu, J., Glatman Zaretsky, A., Haxhinasto, S., Yancopoulos, G. D., Murphy, A. J., Sleeman, M. W., et al. (2023) · Science Advances · doi:10.1126/sciadv.ade4395 · Cited by 56
Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT
Jiang, Y., Benz, T. L., & Long, S. B. (2021) · Science · doi:10.1126/science.abg4998 · Cited by 55
New prediction categories in CASP15
Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R. C., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26515 · Cited by 54
“25 Given two sets of interactions, one for the model and 27,28 It is worth noting that model-independent measures are known to overinflate scores for compressed models with unrealistic geometries.”
BackgroundFragment-based computational design of antibodies targeting structured epitopes
Aguilar Rangel, M., Bedwell, A., Costanzi, E., Taylor, R. J., Russo, R., Bernardes, G. J. L., Ricagno, S., Frydman, J., Vendruscolo, M., & Sormanni, P. (2022) · Science Advances · doi:10.1126/sciadv.abp9540 · Cited by 55
Structural organization of the retriever–CCC endosomal recycling complex
Boesch, D. J., Singla, A., Han, Y., Kramer, D. A., Liu, Q., Suzuki, K., Juneja, P., Zhao, X., Long, X., Medlyn, M. J., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01184-4 · Cited by 52
Cryo-EM structure of the cytosolic AhR complex.
Wen, Z., Zhang, Y., Zhang, B., Hang, Y., Xu, L., Chen, Y., Xie, Q., Zhao, Q., Zhang, L., Li, G., et al. (2023) · Structure · doi:10.1016/j.str.2022.12.013 · Cited by 51
Barbarin-Bocahu, I., & Graille, M. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322002157 · Cited by 52
Cryptochrome–Timeless structure reveals circadian clock timing mechanisms
Lin, C., Feng, S., DeOliveira, C. C., & Crane, B. R. (2023) · Nature · doi:10.1038/s41586-023-06009-4 · Cited by 51
Bahar, M. W., Porta, C., Fox, H., Macadam, A. J., Fry, E. E., & Stuart, D. I. (2021) · npj Vaccines · doi:10.1038/s41541-020-00267-3 · Cited by 42
STK19 positions TFIIH for cell-free transcription-coupled DNA repair
Mevissen, T. E. T., Kümmecke, M., Schmid, E. W., Farnung, L., & Walter, J. C. (2024) · Cell · doi:10.1016/j.cell.2024.10.020 · Cited by 50
Jette, C. A., Barnes, C. O., Kirk, S. M., Melillo, B., Smith, A. B., & Bjorkman, P. J. (2021) · Nature Communications · doi:10.1038/s41467-021-21816-x · Cited by 38
FOXP3 recognizes microsatellites and bridges DNA through multimerization
Zhang, W., Leng, F., Wang, X., Ramirez, R. N., Park, J., Benoist, C., & Hur, S. (2023) · Nature · doi:10.1038/s41586-023-06793-z · Cited by 42
Obana, N., Takada, H., Crowe-McAuliffe, C., Iwamoto, M., Egorov, A. A., Wu, K. J. Y., Chiba, S., Murina, V., Paternoga, H., Tresco, B. I. C., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad193 · Cited by 42
Marcyk, P. T., LeBlanc, E. V., Kuntz, D. A., Xue, A., Ortiz, F., Trilles, R., Bengtson, S., Kenney, T. M. G., Huang, D. S., Robbins, N., et al. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01777 · Cited by 40
Structural basis for activation of fungal sterol receptor Upc2 and azole resistance
Tan, L., Chen, L., Yang, H., Jin, B., Kim, G., & Im, Y. J. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-01117-0 · Cited by 38
Peter, M. F., Depping, P., Schneberger, N., Severi, E., Gatterdam, K., Tindall, S., Durand, A., Heinz, V., Koenig, P.-A., Geyer, M., et al. (2021) · doi:10.1101/2021.12.03.471092 · Cited by 38
From primordial clocks to circadian oscillators
Pitsawong, W., Pádua, R. A. P., Grant, T., Hoemberger, M., Otten, R., Bradshaw, N., Grigorieff, N., & Kern, D. (2023) · Nature · doi:10.1038/s41586-023-05836-9 · Cited by 37
Structure of the immunoregulatory sialidase NEU1
Gorelik, A., Illes, K., Mazhab-Jafari, M. T., & Nagar, B. (2023) · Science Advances · doi:10.1126/sciadv.adf8169 · Cited by 36
Vuckovic, Z., Wang, J., Pham, V., Mobbs, J. I., Belousoff, M. J., Bhattarai, A., Burger, W. A., Thompson, G., Yeasmin, M., Nawaratne, V., et al. (2023) · eLife · doi:10.7554/elife.83477 · Cited by 34
Structural basis for plasmid restriction by SMC JET nuclease
Roisné-Hamelin, F., Liu, H. W., Taschner, M., Li, Y., & Gruber, S. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.01.009 · Cited by 34
Sun, X., Jing, L., Li, F., Zhang, M., Diao, X., Zhuang, J., Rastinejad, F., & Wu, D. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2208804119 · Cited by 32
Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III
Di Trani, J. M., Liu, Z., Whitesell, L., Brzezinski, P., Cowen, L. E., & Rubinstein, J. L. (2022) · Structure · doi:10.1016/j.str.2021.08.006 · Cited by 32
Li, B., Hoel, C. M., & Brohawn, S. G. (2021) · Nature Communications · doi:10.1038/s41467-021-27283-8 · Cited by 31
Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Chen, X., Ali, Y. I., Fisher, C. E., Arribas-Bosacoma, R., Rajasekaran, M. B., Williams, G., Walker, S., Booth, J. R., Hudson, J. J., Roe, S. M., et al. (2021) · eLife · doi:10.7554/elife.65339 · Cited by 34
Liu, S., Xia, X., Zhen, J., Li, Z., & Zhou, Z. H. (2022) · Cell Discovery · doi:10.1038/s41421-022-00487-y · Cited by 29
Molecular basis of FIGNL1 in dissociating RAD51 from DNA and chromatin
Carver, A., Yu, T.-Y., Yates, L. A., White, T., Wang, R., Lister, K., Jasin, M., & Zhang, X. (2025) · Science · doi:10.1126/science.adr7920 · Cited by 25
Khan, N., Pelletier, D., McAlear, T. S., Croteau, N., Veyron, S., Bayne, A. N., Black, C., Ichikawa, M., Khalifa, A. A. Z., Chaaban, S., et al. (2021) · Structure · doi:10.1016/j.str.2021.01.001 · Cited by 24
A cereblon-based glue degrader of NEK7 regulates NLRP3 inflammasome in a context-dependent manner
Sylvain, A., Stoehr, N., Ma, F., Cernijenko, A., Schröder, M., Khoshouei, M., Vogelsanger, M., Schoenboerner, M., Burke, A., Rao, P., et al. (2025) · Cell Chemical Biology · doi:10.1016/j.chembiol.2025.06.005 · Cited by 23
Structural basis for Retriever-SNX17 assembly and endosomal sorting
Singla, A., Boesch, D. J., Fung, H. Y. J., Ngoka, C., Enriquez, A. S., Song, R., Kramer, D. A., Han, Y., Banarer, E., Lemoff, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54583-6 · Cited by 23
PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation
Dhingra, Y., Suresh, S. K., Juneja, P., & Sashital, D. G. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.09.030 · Cited by 21
Polymerization of ZBTB transcription factors regulates chromatin occupancy
Park, P. M. C., Park, J., Brown, J., Hunkeler, M., Roy Burman, S. S., Donovan, K. A., Yoon, H., Nowak, R. P., Słabicki, M., Ebert, B. L., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.06.010 · Cited by 22
Wang, M., Li, T., Ouyang, Z., Tang, K., Zhu, Y., Song, C., Sun, H., Yu, B., Ji, X., & Sun, Y. (2022) · iScience · doi:10.1016/j.isci.2022.104009 · Cited by 20
Koide, E., Pietz, H. L., Beltran, J., & Chen, J. (2025) · Nature Communications · doi:10.1038/s41467-024-55810-w · Cited by 17
Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome
Pandey, K. K., Bera, S., Shi, K., Rau, M. J., Oleru, A. V., Fitzpatrick, J. A. J., Engelman, A. N., Aihara, H., & Grandgenett, D. P. (2021) · Communications Biology · doi:10.1038/s42003-021-01855-2 · Cited by 14
T cell toxicity induced by tigecycline binding to the mitochondrial ribosome
Shao, Q., Khawaja, A., Nguyen, M. D., Singh, V., Zhang, J., Liu, Y., Nordin, J., Adori, M., Axel Innis, C., Castro Dopico, X., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59388-9 · Cited by 16
Kerrigan, J. R., Thomsen, N. M., Cernijenko, A., Kochanek, S. E., Dewhurst, J., O’Brien, G., Ware, N. F., Sanchez, C. C., Manning, J. R., Ma, X., et al. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c02251 · Cited by 15
Structural basis of microtubule-mediated signal transduction
Choi, S. R., Blum, T. B., Giono, M., Roy, B., Vakonakis, I., Schmid, D., Oelgarth, N., Ranganathan, A., Gossert, A. D., Shivashankar, G. V., et al. (2026) · Cell · doi:10.1016/j.cell.2025.11.011 · Cited by 14
Metadata
- Authors
- Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., Terwilliger, T. C., Urzhumtsev, A. G., Videau, L. L., Williams, C. J., & Adams, P. D.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2019-10-01
- Volume
- 75
- Issue
- 10
- Pages
- 861-877
- ISSN
- 2059-7983
- PMC
- PMC6778852
- Cited by
- 7,953
- References
- 5
- Licence
- Funders
- National Institutes of Health (P01GM063210, 1R01GM071939)
- US Department of Energy (DE-AC02-05CH1123.)
- Wellcome Trust (209407/Z/17/Z)
- Horizon 2020 (790122)
- French Infrastructure for Integrated Structural Biology (ANR-10-INBS-05)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
