Version 1.2 of the Crystallography and NMR system

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187

Towards 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

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Langer, G., Cohen, S. X., Lamzin, V. S., & Perrakis, A. (2008) · Nature Protocols · doi:10.1038/nprot.2008.91 · Cited by 1,606

Current Status of the AMOEBA Polarizable Force Field

Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., et al. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp910674d · Cited by 1,440

Unified Polymerization Mechanism for the Assembly of ASC-Dependent Inflammasomes

Lu, A., Magupalli, V. G., Ruan, J., Yin, Q., Atianand, M. K., Vos, M. R., Schröder, G. F., Fitzgerald, K. A., Wu, H., & Egelman, E. H. (2014) · Cell · doi:10.1016/j.cell.2014.02.008 · Cited by 1,353

Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA

Chandra, V., Huang, P., Hamuro, Y., Raghuram, S., Wang, Y., Burris, T. P., & Rastinejad, F. (2008) · Nature · doi:10.1038/nature07413 · Cited by 808

Crystal structure of the entire respiratory complex I

Baradaran, R., Berrisford, J. M., Minhas, G. S., & Sazanov, L. A. (2013) · Nature · doi:10.1038/nature11871 · Cited by 797

Sequence co-evolution gives 3D contacts and structures of protein complexes

Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife · doi:10.7554/elife.03430 · Cited by 515

Structure of a complex of the ATPase SecA and the protein-translocation channel.

Zimmer, J., Nam, Y., & Rapoport, T. A. (2008) · Nature · doi:10.1038/nature07335 · Cited by 459

Distance-based protein folding powered by deep learning

Xu, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1821309116 · Cited by 401

Structure of the membrane domain of respiratory complex I

Efremov, R. G., & Sazanov, L. A. (2011) · Nature · doi:10.1038/nature10330 · Cited by 370

Architecture of the synaptotagmin–SNARE machinery for neuronal exocytosis

Zhou, Q., Lai, Y., Bacaj, T., Zhao, M., Lyubimov, A. Y., Uervirojnangkoorn, M., Zeldin, O. B., Brewster, A. S., Sauter, N. K., Cohen, A. E., et al. (2015) · Nature · doi:10.1038/nature14975 · Cited by 348

Structural aspects of messenger RNA reading frame maintenance by the ribosome

Jenner, L. B., Demeshkina, N., Yusupova, G., & Yusupov, M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1790 · Cited by 312

Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases

Canning, P., Cooper, C. D. O., Krojer, T., Murray, J. W., Pike, A. C. W., Chaikuad, A., Keates, T., Thangaratnarajah, C., Hojzan, V., Marsden, B. D., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.437996 · Cited by 284

Structural basis for protein antiaggregation activity of the trigger factor chaperone.

Saio, T., Guan, X., Rossi, P., Economou, A., & Kalodimos, C. G. (2014) · Science · doi:10.1126/science.1250494 · Cited by 289

Conformational states dynamically populated by a kinase determine its function

Xie, T., Saleh, T., Rossi, P., & Kalodimos, C. G. (2020) · Science · doi:10.1126/science.abc2754 · Cited by 266

Teaching an Old Scaffold New Tricks: Monobodies Constructed Using Alternative Surfaces of the FN3 Scaffold

Koide, A., Wojcik, J., Gilbreth, R. N., Hoey, R. J., & Koide, S. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.12.019 · Cited by 227

Deep Learning in Protein Structural Modeling and Design

Gao, W., Mahajan, S. P., Sulam, J., & Gray, J. J. (2020) · Patterns · doi:10.1016/j.patter.2020.100142 · Cited by 227

Structure and insights into the function of a Ca2+-activated Cl− channel

Kane Dickson, V., Pedi, L., & Long, S. B. (2014) · Nature · doi:10.1038/nature13913 · Cited by 202

Single-molecule FRET–derived model of the synaptotagmin 1–SNARE fusion complex

Choi, U. B., Strop, P., Vrljic, M., Chu, S., Brunger, A. T., & Weninger, K. R. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1763 · Cited by 197

Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist

Masureel, M., Zou, Y., Picard, L.-P., van der Westhuizen, E., Mahoney, J. P., Rodrigues, J. P. G. L. M., Mildorf, T. J., Dror, R. O., Shaw, D. E., Bouvier, M., et al. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0145-x · Cited by 194

Structural basis of receptor sharing by interleukin 17 cytokines

Ely, L. K., Fischer, S., & Garcia, K. C. (2009) · Nature Immunology · doi:10.1038/ni.1813 · Cited by 195

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

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

Greener, J. G., Kandathil, S. M., & Jones, D. T. (2019) · Nature Communications · doi:10.1038/s41467-019-11994-0 · Cited by 178

Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery

Oberoi, J., Fairall, L., Watson, P. J., Yang, J.-C., Czimmerer, Z., Kampmann, T., Goult, B. T., Greenwood, J. A., Gooch, J. T., Kallenberger, B. C., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1983 · Cited by 165

Structural insights into the assembly and activation of IL-1β with its receptors

Wang, D., Zhang, S., Li, L., Liu, X., Mei, K., & Wang, X. (2010) · Nature Immunology · doi:10.1038/ni.1925 · Cited by 162

Loops Govern SH2 Domain Specificity by Controlling Access to Binding Pockets

Kaneko, T., Huang, H., Zhao, B., Li, L., Liu, H., Voss, C. K., Wu, C., Schiller, M. R., & Li, S. S.-C. (2010) · Science Signaling · doi:10.1126/scisignal.2000796 · Cited by 146

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

Green, A. G., Elhabashy, H., Brock, K. P., Maddamsetti, R., Kohlbacher, O., & Marks, D. S. (2021) · Nature Communications · doi:10.1038/s41467-021-21636-z · Cited by 114

Capturing a substrate in an activated RING E3/E2–SUMO complex

Streich Jr, F. C., & Lima, C. D. (2016) · Nature · doi:10.1038/nature19071 · Cited by 108

Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A

Singh, K., Gittis, A. G., Nguyen, P., Gowda, D. C., Miller, L. H., & Garboczi, D. N. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1479 · Cited by 99

Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis

Chim, N., Iniguez, A., Nguyen, T. Q., & Goulding, C. W. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.11.025 · Cited by 102

A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors

Pyburn, T. M., Bensing, B. A., Xiong, Y. Q., Melancon, B. J., Tomasiak, T. M., Ward, N. J., Yankovskaya, V., Oliver, K. M., Cecchini, G., Sulikowski, G. A., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002112 · Cited by 84

Structural basis for recruitment of Rab6-interacting protein 1 to Golgi via a RUN domain

Recacha, R., Boulet, A., Jollivet, F., Monier, S., Houdusse, A., Goud, B., & Khan, A. R. (2009) · Structure · doi:10.1016/j.str.2008.10.014 · Cited by 83

A role for USP7 in DNA replication.

Jagannathan, M., Nguyen, T., Gallo, D., Luthra, N., Brown, G. W., Saridakis, V., & Frappier, L. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.00639-13 · Cited by 71

Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase

Gupta, K., Turkki, V., Sherrill-Mix, S., Hwang, Y., Eilers, G., Taylor, L., McDanal, C., Wang, P., Temelkoff, D., Nolte, R. T., et al. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002584 · Cited by 68

ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat

Nishio, S., Emori, C., Wiseman, B., Fahrenkamp, D., Dioguardi, E., Zamora-Caballero, S., Bokhove, M., Han, L., Stsiapanava, A., Algarra, B., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.013 · Cited by 54

Assessment of prediction methods for protein structures determined by NMR in CASP14 : Impact of AlphaFold2

Huang, Y. J., Zhang, N., Bersch, B., Fidelis, K., Inouye, M., Ishida, Y., Kryshtafovych, A., Kobayashi, N., Kuroda, Y., Liu, G., et al. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26246 · Cited by 49

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach

Henry, N., Krammer, E.-M., Stengel, F., Adams, Q., Van Liefferinge, F., Hubin, E., Chaves, R., Efremov, R., Aebersold, R., Vandenbussche, G., et al. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006165 · Cited by 42

Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2

Cantara, W. A., Bilbille, Y., Kim, J., Kaiser, R., Leszczyńska, G., Malkiewicz, A., & Agris, P. F. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.12.054 · Cited by 36

Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications

Goydel, R. S., Weber, J., Peng, H., Qi, J., Soden, J., Freeth, J., Park, H., & Rader, C. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.012791 · Cited by 34

Mutants of Cytochrome P450 Reductase Lacking Either Gly-141 or Gly-143 Destabilize Its FMN Semiquinone

Rwere, F., Xia, C., Im, S., Haque, M. M., Stuehr, D. J., Waskell, L., & Kim, J.-J. P. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.724625 · Cited by 26

Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex

Foucher, A.-E., Touat-Todeschini, L., Juarez-Martinez, A. B., Rakitch, A., Laroussi, H., Karczewski, C., Acajjaoui, S., Soler-López, M., Cusack, S., Mackereth, C. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32542-3 · Cited by 26

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Soltanikazemi, E., Quadir, F., Roy, R. S., Guo, Z., & Cheng, J. (2022) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26269 · Cited by 15

Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling

(2022) · doi:10.1038/s42003-022-03411-y · Cited by 14

Identification and Characterization of Novel Inhibitors of Mammalian Aspartyl Aminopeptidase

Chen, Y., Tang, H., Seibel, W., Papoian, R., Oh, K., Li, X., Zhang, J., Golczak, M., Palczewski, K., & Kiser, P. D. (2014) · Molecular Pharmacology · doi:10.1124/mol.114.093070 · Cited by 14

The 2.3 Å Structure of A21, a Protein Component of the Conserved Poxvirus Entry-Fusion Complex

Diesterbeck, U. S., Muslinkina, L. A., Gittis, A. G., Singh, K., Moss, B., & Garboczi, D. N. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169097 · Cited by 9

Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin

Thore, S., Raoelijaona, F., Talenton, V., Fribourg, S., & Mackereth, C. D. (2023) · Open Biology · doi:10.1098/rsob.230221 · Cited by 6

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

Chen, D. F., Roe, L. T., Yuping, L., Borges, A. L., Zhang, J. Y., Babbar, P., Maji, S., Stevens, M. G. V., Correy, G. J., Diolaiti, M. E., et al. (2025) · mBio · doi:10.1128/mbio.01698-25 · Cited by 4