Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

VMD: visual molecular dynamics

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Scalable molecular dynamics with NAMD

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Stability and dynamics of virus capsids described by coarse-grained modeling

Arkhipov, A., Freddolino, L., & Schulten, K. (2006) · Structure · doi:10.1016/j.str.2006.10.003 · Cited by 262

A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2

Chi, X., Yan, R., Zhang, J., Zhang, G., Zhang, Y., Hao, M., Zhang, Z., Fan, P., Dong, Y., Yang, Y., et al. (2020) · Science · doi:10.1126/science.abc6952 · Cited by 1,385

Structure and mechanogating mechanism of the Piezo1 channel

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Outcome of the first electron microscopy validation task force meeting

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Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

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Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase

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Cryo-EM structures of the TMEM16A calcium-activated chloride channel

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Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.

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Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

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Structure of the membrane-assembled retromer coat determined by cryo-electron tomography

Kovtun, O., Leneva, N., Bykov, Y. S., Ariotti, N., Teasdale, R. D., Schaffer, M., Engel, B. D., Owen, D. J., Briggs, J. A. G., & Collins, B. M. (2018) · Nature · doi:10.1038/s41586-018-0526-z · Cited by 247

Visualizing translation dynamics at atomic detail inside a bacterial cell

Xue, L., Lenz, S., Zimmermann-Kogadeeva, M., Tegunov, D., Cramer, P., Bork, P., Rappsilber, J., & Mahamid, J. (2022) · Nature · doi:10.1038/s41586-022-05255-2 · Cited by 184

Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils

Röder, C., Kupreichyk, T., Gremer, L., Schäfer, L. U., Pothula, K. R., Ravelli, R. B. G., Willbold, D., Hoyer, W., & Schröder, G. F. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0442-4 · Cited by 180

Comprehensive structure and functional adaptations of the yeast nuclear pore complex

Akey, C. W., Singh, D., Ouch, C., Echeverria, I., Nudelman, I., Varberg, J. M., Yu, Z., Fang, F., Shi, Y., Wang, J., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.015 · Cited by 180

Structures of rhodopsin in complex with G-protein-coupled receptor kinase 1

Chen, Q., Plasencia, M., Li, Z., Mukherjee, S., Patra, D., Chen, C.-L., Klose, T., Yao, X.-Q., Kossiakoff, A. A., Chang, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03721-x · Cited by 152

Structure of the SecY channel during initiation of protein translocation

Park, E., Ménétret, J.-F., Gumbart, J. C., Ludtke, S. J., Li, W., Whynot, A., Rapoport, T. A., & Akey, C. W. (2014) · Nature · doi:10.1038/nature12720 · Cited by 148

In situ architecture of the ER–mitochondria encounter structure

Wozny, M. R., Di Luca, A., Morado, D. R., Picco, A., Khaddaj, R., Campomanes, P., Ivanović, L., Hoffmann, P. C., Miller, E. A., Vanni, S., et al. (2023) · Nature · doi:10.1038/s41586-023-06050-3 · Cited by 134

Structural and functional insights into the mode of action of a universally conserved Obg GTPase.

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Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly

Bharat, T. A. M., Castillo Menendez, L. R., Hagen, W. J. H., Lux, V., Igonet, S., Schorb, M., Schur, F. K. M., Kräusslich, H.-G., & Briggs, J. A. G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401455111 · Cited by 107

Structure and Response to Flow of the Glycocalyx Layer

Cruz-Chu, E. R., Malafeev, A., Pajarskas, T., Pivkin, I. V., & Koumoutsakos, P. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2013.09.060 · Cited by 87

Vimentin filaments integrate low-complexity domains in a complex helical structure

Eibauer, M., Weber, M. S., Kronenberg-Tenga, R., Beales, C. T., Boujemaa-Paterski, R., Turgay, Y., Sivagurunathan, S., Kraxner, J., Köster, S., Goldman, R. D., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01261-2 · Cited by 87

Cryo‐EM model validation using independent map reconstructions

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Progressive assembly of multi-domain protein structures from cryo-EM density maps

Zhou, X., Li, Y., Zhang, C., Zheng, W., Zhang, G., & Zhang, Y. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00232-1 · Cited by 75

Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding

Wang, K., Dagil, R., Lavstsen, T., Misra, S. K., Spliid, C. B., Wang, Y., Gustavsson, T., Sandoval, D. R., Vidal-Calvo, E. E., Choudhary, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23254-1 · Cited by 52

Integrative Structural Biology in the Era of Accurate Structure Prediction

Masrati, G., Landau, M., Ben-Tal, N., Lupas, A., Kosloff, M., & Kosinski, J. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167127 · Cited by 53

Structural basis for regulated assembly of the mitochondrial fission GTPase Drp1

Rochon, K., Bauer, B. L., Roethler, N. A., Buckley, Y., Su, C.-C., Huang, W., Ramachandran, R., Stoll, M. S. K., Yu, E. W., Taylor, D. J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45524-4 · Cited by 52

Structure of ATP synthase under strain during catalysis

Guo, H., & Rubinstein, J. L. (2022) · Nature Communications · doi:10.1038/s41467-022-29893-2 · Cited by 51

Structure of human TRPM8 channel

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The structure of apolipoprotein B100 from human low-density lipoprotein

Berndsen, Z. T., & Cassidy, C. K. (2025) · Nature · doi:10.1038/s41586-024-08467-w · Cited by 43

Molecular dynamics of EF‐G during translocation

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Rational exploration of fold atlas for human solute carrier proteins

Xie, T., Chi, X., Huang, B., Ye, F., Zhou, Q., & Huang, J. (2022) · Structure · doi:10.1016/j.str.2022.05.015 · Cited by 23

Integrated model of the vertebrate augmin complex

Travis, S. M., Mahon, B. P., Huang, W., Ma, M., Rale, M. J., Kraus, J., Taylor, D. J., Zhang, R., & Petry, S. (2023) · Nature Communications · doi:10.1038/s41467-023-37519-4 · Cited by 16

Cryo-EM reveals the conformational epitope of human monoclonal antibody PAM1.4 broadly reacting with polymorphic malarial protein VAR2CSA

Raghavan, S. S. R., Dagil, R., Lopez-Perez, M., Conrad, J., Bassi, M. R., Quintana, M. D. P., Choudhary, S., Gustavsson, T., Wang, Y., Gourdon, P., et al. (2022) · PLOS Pathogens · doi:10.1371/journal.ppat.1010924 · Cited by 14

Cryo-EM structure of the human Asc-1 transporter complex

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The Structure of the Drp1 Lattice on Membrane

Peng, R., Rochon, K., Hutson, A. N., Stagg, S. M., & Mears, J. A. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169125 · Cited by 12

Automated simulation-based membrane protein refinement into cryo-EM data

Yvonnesdotter, L., Rovšnik, U., Blau, C., Lycksell, M., Howard, R. J., & Lindahl, E. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2023.05.033 · Cited by 6

Dimerization of GAS2 mediates crosslinking of microtubules and F-actin

An, J., Imasaki, T., Narita, A., Niwa, S., Sasaki, R., Makino, T., Nitta, R., & Kikkawa, M. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00415-2 · Cited by 5

Rational Exploration of Fold Atlas for Human Solute Carrier Proteins

Xie, T., Chi, X., Huang, B., Ye, F., Zhou, Q., & Huang, J. (2021) · doi:10.1101/2021.08.21.457230