Integrative Structural Biology in the Era of Accurate Structure Prediction
Open accessAbstract
Characterizing the three-dimensional structure of macromolecules is central to understanding their function. Traditionally, structures of proteins and their complexes have been determined using experimental techniques such as X-ray crystallography, NMR, or cryo-electron microscopy-applied individually or in an integrative manner. Meanwhile, however, computational methods for protein structure prediction have been improving their accuracy, gradually, then suddenly, with the breakthrough advance by AlphaFold2, whose models of monomeric proteins are often as accurate as experimental structures. This breakthrough foreshadows a new era of computational methods that can build accurate models for most monomeric proteins. Here, we envision how such accurate modeling methods can combine with experimental structural biology techniques, enhancing integrative structural biology. We highlight the challenges that arise when considering multiple structural conformations, protein complexes, and polymorphic assemblies. These challenges will motivate further developments, both in modeling programs and in methods to solve experimental structures, towards better and quicker investigation of structure-function relationships.
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
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?
AlphaFold and RoseTTAfold accurately assess their confidence at the level of individual residues and interdomain contacts.
“The programs were also shown to accurately assess their confidence at the level of individual residues and interdomain contacts (27,28,62).”
From AI-based structure prediction empowers integrative structural analysis of human nuclear pores (2022) · cites this paper as [62]
AlphaFold and RoseTTAfold have demonstrated unprecedented accuracy in predicting structures of complexes.
“However, AlphaFold and RoseTTAfold have recently demonstrated unprecedented accuracy in predicting structures of monomeric proteins (27,28,(61)(62)(63)(64)(65)(66) and complexes (35,62,67,68).”
From AI-based structure prediction empowers integrative structural analysis of human nuclear pores (2022) · cites this paper as [62]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996012255 · Cited by 14,671 · see citing works
Mastering the game of Go without human knowledge
Silver, D., Schrittwieser, J., Simonyan, K., Antonoglou, I., Huang, A., Guez, A., Hubert, T., Baker, L., Lai, M., Bolton, A., et al. (2017) · Nature · doi:10.1038/nature24270 · Cited by 9,084 · see citing works
Principles that Govern the Folding of Protein Chains
Anfinsen, C. B. (1973) · Science · doi:10.1126/science.181.4096.223 · Cited by 7,096 · see citing works
International Conference on Learning Representations (ICLR 2013)
松尾, 豊. (2013) · 人工知能学会誌 = Journal of Japanese Society for Artificial Intelligence · Cited by 6,286 · see citing works
I-TASSER: a unified platform for automated protein structure and function prediction
Roy, A., Küçükural, A., & Zhang, Y. (2010) · Nature Protocols · doi:10.1038/nprot.2010.5 · Cited by 6,093 · see citing works
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 5,542 · see citing works
Announcing the worldwide Protein Data Bank
Berman, H., Henrick, K., & Nakamura, H. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1203-980 · Cited by 3,093 · see citing works
Über einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt
Einstein, A. (1905) · Annalen der Physik · doi:10.1002/andp.19053220607 · Cited by 3,090 · see citing works
Automated MAD and MIR structure solution
Terwilliger, T. C., & Berendzen, J. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444999000839 · Cited by 3,038 · see citing works
A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure
Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991) · Science · doi:10.1126/science.1853201 · Cited by 2,851 · see citing works
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
Zimmermann, L., Stephens, A., Nam, S.-Z., Rau, D., Kübler, J., Lozajic, M., Gabler, F., Söding, J., Lupas, A. N., & Alva, V. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.12.007 · Cited by 2,522 · see citing works
Self-citation[16] SHELXL: High-resolution refinement
Sheldrick, G. M., & Schneider, T. R. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77018-6 · Cited by 2,488 · see citing works
Efficient generation of mouse models of human diseases via ABE- and BE-mediated base editing
Liu, Z., Lu, Z., Yang, G., Huang, S., Li, G., Feng, S., Liu, Y., Li, J., Yu, W., Zhang, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04768-7 · Cited by 2,103 · see citing works
Cryo-EM structures of tau filaments from Alzheimer’s disease
Fitzpatrick, A. W. P., Falcon, B., He, S., Murzin, A. G., Murshudov, G., Garringer, H. J., Crowther, R. A., Ghetti, B., Goedert, M., & Scheres, S. H. W. (2017) · Nature · doi:10.1038/nature23002 · Cited by 2,061 · see citing works
Common core structure of amyloid fibrils by synchrotron X-ray diffraction.
Sunde, M., Serpell, L., Bartlam, M., Fraser, P., Pepys, M., & Blake, C. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1348 · Cited by 1,666 · see citing works
Maximum-likelihood density modification
Terwilliger, T. C. (2000) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444900005072 · Cited by 1,637 · see citing works
Substructure solution withSHELXD
Schneider, T. R., & Sheldrick, G. M. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902011678 · Cited by 1,591 · see citing works
The packing of α-helices: simple coiled-coils
Crick, F. H. C. (1953) · Acta Crystallographica · doi:10.1107/s0365110x53001964 · Cited by 1,578 · see citing works
Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L.-W., Read, R. J., & Adams, P. D. (2008) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490705024x · Cited by 1,462 · see citing works
Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D. S., Sander, C., Zecchina, R., Onuchic, J. N., Hwa, T., & Weigt, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111471108 · Cited by 1,434 · see citing works
Kühlbrandt, W. (2014) · Science · doi:10.1126/science.1251652 · Cited by 1,325 · see citing works
Role of Escherichia coli Curli Operons in Directing Amyloid Fiber Formation
Chapman, M., Robinson, L. S., Pinkner, J., Roth, R., Heuser, J., Hammar, M., Normark, S., & Hultgren, S. (2002) · Science · doi:10.1126/science.1067484 · Cited by 1,282 · see citing works
A new approach to protein fold recognition
Jones, D. T., Taylort, W. R., & Thornton, J. M. (1992) · Nature · doi:10.1038/358086a0 · Cited by 1,221 · see citing works
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM
Wagner, T., Merino, F., Stabrin, M., Moriya, T., Antoni, C., Apelbaum, A., Hagel, P., Sitsel, O., Raisch, T., Prumbaum, D., et al. (2019) · Communications Biology · doi:10.1038/s42003-019-0437-z · Cited by 1,217 · see citing works
Molecular structural basis for polymorphism in Alzheimer's β-amyloid fibrils
Paravastu, A. K., Leapman, R. D., Yau, W., & Tycko, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806270105 · Cited by 1,165 · see citing works
Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163 · see citing works
Protein 3D Structure Computed from Evolutionary Sequence Variation
Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144 · see citing works
Determination of Macromolecular Structures from Anomalous Diffraction of Synchrotron Radiation
Hendrickson, W. A. (1991) · Science · doi:10.1126/science.1925561 · Cited by 1,131 · see citing works
Molecular Structure of β-Amyloid Fibrils in Alzheimer’s Disease Brain Tissue
Lu, J., Qiang, W., Yau, W., Schwieters, C. D., Meredith, S. C., & Tycko, R. (2013) · Cell · doi:10.1016/j.cell.2013.08.035 · Cited by 1,087 · see citing works
Functional Amyloids As Natural Storage of Peptide Hormones in Pituitary Secretory Granules
Maji, S. K., Perrin, M. H., Sawaya, M. R., Jessberger, S., Vadodaria, K. C., Rissman, R. A., Singru, P. S., Nilsson, K. P. R., Simon, R. A., Schubert, D. A., et al. (2009) · Science · doi:10.1126/science.1173155 · Cited by 1,051 · see citing works
Fibril structure of amyloid-β(1–42) by cryo–electron microscopy
Gremer, L., Schölzel, D., Schenk, C., Reinartz, E., Labahn, J., Ravelli, R. B. G., Tusche, M., López‐Iglesias, C., Hoyer, W., Heise, H., et al. (2017) · Science · doi:10.1126/science.aao2825 · Cited by 1,031 · see citing works
Identification of direct residue contacts in protein–protein interaction by message passing
Weigt, M., White, R. A., Szurmant, H., Hoch, J. A., & Hwa, T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805923106 · Cited by 1,025 · see citing works
A new era for understanding amyloid structures and disease
Iadanza, M. G., Jackson, M. P., Hewitt, E. W., Ranson, N. A., & Radford, S. E. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0060-8 · Cited by 969 · see citing works
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Wang, S., Sun, S., Li, Z., Zhang, R., & Xu, J. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005324 · Cited by 931 · see citing works
Single-particle cryo-EM at atomic resolution
Nakane, T., Kotecha, A., Sente, A., McMullan, G., Masiulis, S., Brown, P. M. G. E., Grigoras, I. T., Malinauskaitė, L., Malinauskas, T., Miehling, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2829-0 · Cited by 881 · see citing works
The detection of sub-units within the crystallographic asymmetric unit
Rossmann, M. G., & Blow, D. M. (1962) · Acta Crystallographica · doi:10.1107/s0365110x62000067 · Cited by 874 · see citing works
Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
Trabuco, L. G., Villa, E., Mitra, K., Frank, J., & Schulten, K. J. (2008) · Structure · doi:10.1016/j.str.2008.03.005 · Cited by 866 · see citing works
Xu, D. H., & Zhang, Y. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24065 · Cited by 853 · see citing works
Hydrogen exchange mass spectrometry for studying protein structure and dynamics
Konermann, L., Pan, J., & Liu, Y. (2010) · Chemical Society Reviews · doi:10.1039/c0cs00113a · Cited by 842 · see citing works
Structures of filaments from Pick’s disease reveal a novel tau protein fold
Falcon, B., Zhang, W., Murzin, A. G., Murshudov, G. N., Garringer, H. J., Vidal, R., Crowther, R. A., Ghetti, B. F., Scheres, S. H. W., & Goedert, M. (2018) · Nature · doi:10.1038/s41586-018-0454-y · Cited by 837 · see citing works
Functional Amyloid Formation within Mammalian Tissue
Fowler, D. M., Koulov, A. V., Alory, C., Marks, M. S., Balch, W. E., & Kelly, J. W. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0040006 · Cited by 824 · see citing works
Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M. M., Nussinov, R., & Ishii, Y. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2991 · Cited by 822 · see citing works
Pushing the boundaries of molecular replacement with maximum likelihood
Read, R. J. (2001) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444901012471 · Cited by 822 · see citing works
Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils
Colvin, M. T., Silvers, R., Ni, Q. Z., Can, T. V., Sergeyev, I. V., Rosay, M., Donovan, K. J., Michael, B. C., Wall, J. S., Linse, S. S., et al. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b05129 · Cited by 812 · see citing works
Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril
Wälti, M. A., Ravotti, F., Arai, H., Glabe, C. G., Wall, J. S., Böckmann, A., Güntert, P., Meier, B. H., & Riek, R. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600749113 · Cited by 810 · see citing works
Structures of α-synuclein filaments from multiple system atrophy
Schweighauser, M., Shi, Y., Tarutani, A., Kametani, F., Murzin, A. G., Ghetti, B. F., Matsubara, T., Tomita, T., Ando, T., Hasegawa, K., et al. (2020) · Nature · doi:10.1038/s41586-020-2317-6 · Cited by 776 · see citing works
Atomic-resolution protein structure determination by cryo-EM
Yip, K. M., Fischer, N., Paknia, E., Chari, A., & Stark, H. (2020) · Nature · doi:10.1038/s41586-020-2833-4 · Cited by 750 · see citing works
Ramachandran, G. N., & Kartha, G. (1955) · Nature · doi:10.1038/176593a0 · Cited by 741 · see citing works
Murray, D. T., Kato, M., Lin, Y., Thurber, K. R., Hung, I., McKnight, S. L., & Tycko, R. (2017) · Cell · doi:10.1016/j.cell.2017.08.048 · Cited by 740 · see citing works
CAPRI: A Critical Assessment of PRedicted Interactions
Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703 · see citing works
Novel tau filament fold in chronic traumatic encephalopathy encloses hydrophobic molecules
Falcon, B., Zivanov, J., Zhang, W., Murzin, A. G., Garringer, H. J., Vidal, R., Crowther, R. A., Newell, K. L., Ghetti, B. F., Goedert, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1026-5 · Cited by 703 · see citing works
Structural variation in amyloid-β fibrils from Alzheimer's disease clinical subtypes
Qiang, W., Yau, W., Lu, J., Collinge, J., & Tycko, R. (2017) · Nature · doi:10.1038/nature20814 · Cited by 634 · see citing works
Structure of the toxic core of α-synuclein from invisible crystals
Rodríguez, J. A., Ivanova, M. I., Sawaya, M. R., Cascio, D., Reyes, F. E., Shi, D., Sangwan, S., Guenther, E. L., Johnson, L. M., Zhang, M., et al. (2015) · Nature · doi:10.1038/nature15368 · Cited by 629 · see citing works
Cryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernel
Li, B., Ge, P., Murray, K. A., Sheth, P., Zhang, M., Nair, G., Sawaya, M. R., Shin, W. S., Boyer, D. R., Ye, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05971-2 · Cited by 623 · see citing works
The Pleated Sheet, A New Layer Configuration of Polypeptide Chains
Pauling, L. C., & Corey, R. B. (1951) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.37.5.251 · Cited by 602 · see citing works
Cryo-EM structure of alpha-synuclein fibrils
Guerrero-Ferreira, R., Taylor, N. M. I., Mona, D., Ringler, P., Lauer, M. E., Riek, R., Britschgi, M., & Stahlberg, H. (2018) · eLife · doi:10.7554/elife.36402 · Cited by 600 · see citing works
Cryo-EM structure and polymorphism of Aβ amyloid fibrils purified from Alzheimer’s brain tissue
Kollmer, M., Close, W., Funk, L., Rasmussen, J., Bsoul, A., Schierhorn, A., Schmidt, M., Sigurdson, C. J., Jucker, M., & Fändrich, M. (2019) · Nature Communications · doi:10.1038/s41467-019-12683-8 · Cited by 593 · see citing works
Structure of the human voltage-dependent anion channel
Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., & Zeth, K. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808115105 · Cited by 588 · see citing works
A Primer to Single-Particle Cryo-Electron Microscopy
Cheng, Y., Grigorieff, N., Penczek, P. A., & Walz, T. (2015) · Cell · doi:10.1016/j.cell.2015.03.050 · Cited by 570 · see citing works
A large‐scale experiment to assess protein structure prediction methods
Moult, J., Pedersen, J. T., Judson, R., & Fidelis, K. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340230303 · Cited by 555 · see citing works
Novel tau filament fold in corticobasal degeneration
Zhang, W., Tarutani, A., Newell, K. L., Murzin, A. G., Matsubara, T., Falcon, B., Vidal, R., Garringer, H. J., Shi, Y., Ikeuchi, T., et al. (2020) · Nature · doi:10.1038/s41586-020-2043-0 · Cited by 546 · see citing works
3D Electron Diffraction: The Nanocrystallography Revolution
Gemmi, M., Mugnaioli, E., Gorelik, T. E., et al. (2019) · ACS Central Science · doi:10.1021/acscentsci.9b00394 · Cited by 535 · see citing works
The molecular sociology of the cell
Robinson, C. V., Šali, A., & Baumeister, W. P. (2007) · Nature · doi:10.1038/nature06523 · Cited by 533 · see citing works
On the Structure of Native, Denatured, and Coagulated Proteins
Mirsky, A. E., & Pauling, L. C. (1936) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.22.7.439 · Cited by 521 · see citing works
Rich, A. S., & Crick, F. H. C. (1955) · Nature · doi:10.1038/176915a0 · Cited by 516 · see citing works
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 · see citing works
Structural Studies of Amyloid Proteins at the Molecular Level
Eisenberg, D. S., & Sawaya, M. R. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-045104 · Cited by 513 · see citing works
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells
Tegunov, D., Xue, L., Dienemann, C., Cramer, P., & Mahamid, J. (2021) · Nature Methods · doi:10.1038/s41592-020-01054-7 · Cited by 513 · see citing works
Schneidman‐Duhovny, D., Hammel, M., Tainer, J. A., & Šali, A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw389 · Cited by 502 · see citing works
Zhang, W., Falcon, B., Murzin, A. G., Fan, J., Crowther, R. A., Goedert, M., & Scheres, S. H. W. (2019) · eLife · doi:10.7554/elife.43584 · Cited by 500 · see citing works
Integrative structure and functional anatomy of a nuclear pore complex
Kim, S. J., Fernández-Martı́nez, J., Nudelman, I., Shi, Y., Zhang, W., Raveh, B., Herricks, T., Slaughter, B. D., Hogan, J. A., Upla, P., et al. (2018) · Nature · doi:10.1038/nature26003 · Cited by 469 · see citing works
Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks
Hughes, M. P., Sawaya, M. R., Boyer, D. R., Goldschmidt, L., Rodríguez, J. A., Cascio, D., Chong, L., Gonen, T., & Eisenberg, D. S. (2018) · Science · doi:10.1126/science.aan6398 · Cited by 454 · see citing works
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach
Lasker, K., Förster, F. G., Bohn, S., Walzthoeni, T., Villa, E., Unverdorben, P., Beck, F., Aebersold, R. H., Šali, A., & Baumeister, W. P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120559109 · Cited by 442 · see citing works
Compound Helical Configurations of Polypeptide Chains: Structure of Proteins of the α-Keratin Type
Pauling, L. C., & Corey, R. B. (1953) · Nature · doi:10.1038/171059a0 · Cited by 433 · see citing works
Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy
Li, Y., Zhao, C., Luo, F., Liu, Z., Gui, X., Luo, Z., Zhang, X., Li, D., Liu, C., & Li, X. (2018) · Cell Research · doi:10.1038/s41422-018-0075-x · Cited by 432 · see citing works
Structural advances for the major facilitator superfamily (MFS) transporters
Yan, N. (2013) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2013.01.003 · Cited by 418 · see citing works
Three-dimensional electron crystallography of protein microcrystals
Shi, D., Nannenga, B. L., Iadanza, M. G., & Gonen, T. (2013) · eLife · doi:10.7554/elife.01345 · Cited by 408 · see citing works
Polymer principles and protein folding
Dill, K. A. (1999) · Protein Science · doi:10.1110/ps.8.6.1166 · Cited by 404 · see citing works
The formation and stabilization of protein structure
Anfinsen, C. B. (1972) · Biochemical Journal · doi:10.1042/bj1280737 · Cited by 400 · see citing works
Posttranslational Modifications Mediate the Structural Diversity of Tauopathy Strains
Arakhamia, T., Lee, C. E., Carlomagno, Y., Kumar, M., Duong, D. M., Wesseling, H., Kundinger, S. R., Wang, K., Williams, D., Deture, M. A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.01.027 · Cited by 400 · see citing works
Recent atomic models of amyloid fibril structure
Nelson, R. A., & Eisenberg, D. S. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.03.007 · Cited by 393 · see citing works
Protein structure determination in solution by NMR spectroscopy.
Wüthrich, K. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)45665-7 · Cited by 384 · see citing works
Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity
Nogales, E., & Scheres, S. H. W. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.019 · Cited by 381 · see citing works
A database of macromolecular motions
Gerstein, M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.18.4280 · Cited by 375 · see citing works
Extremely high conductivity observed in the triple point topological metal MoP
Kumar, N., Sun, Y., Nicklas, M., Watzman, S. J., Young, O., Leermakers, I., Hornung, J., Klotz, J., Gooth, J., Manna, K., et al. (2019) · RePEc: Research Papers in Economics · Cited by 374 · see citing works
End-to-End Differentiable Learning of Protein Structure
AlQuraishi, M. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.006 · Cited by 371 · see citing works
Tau filaments from multiple cases of sporadic and inherited Alzheimer's disease adopt a common fold
Falcon, B., Zhang, W., Schweighauser, M., Murzin, A. G., Vidal, R., Garringer, H. J., Ghetti, B., Scheres, S. H. W., & Goedert, M. (2018) · Acta Neuropathologica · doi:10.1007/s00401-018-1914-z · Cited by 362 · see citing works
Antiparallel β-sheet architecture in Iowa-mutant β-amyloid fibrils
Qiang, W., Yau, W., Luo, Y., Mattson, M. P., & Tycko, R. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111305109 · Cited by 348 · see citing works
Interferenzerscheinungen bei Röntgenstrahlen
Friedrich, W., Knipping, P., & Laue, M. V. (1913) · Annalen der Physik · doi:10.1002/andp.19133461004 · Cited by 343 · see citing works
Ramachandran, G. N., & Kartha, G. (1954) · Nature · doi:10.1038/174269c0 · Cited by 343 · see citing works
Guerrero-Ferreira, R., Taylor, N. M. I., Arteni, A., Kumari, P., Mona, D., Ringler, P., Britschgi, M., Lauer, M. E., Makky, A., Verasdonck, J., et al. (2019) · eLife · doi:10.7554/elife.48907 · Cited by 338 · see citing works
O'Reilly, F. J., & Rappsilber, J. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0147-0 · Cited by 334 · see citing works
Pmel17 initiates premelanosome morphogenesis within multivesicular bodies
Berson, J. F., Harper, D. C., Tenza, D., Raposo, G., & Marks, M. S. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.11.3451 · Cited by 326 · see citing works
Diversity, biogenesis and function of microbial amyloids
Blanco, L. P., Evans, M. L., Smith, D. R., Badtke, M. P., & Chapman, M. R. (2012) · Trends in Microbiology · doi:10.1016/j.tim.2011.11.005 · Cited by 320 · see citing works
High-resolution structure prediction and the crystallographic phase problem
Qian, B., Raman, S., Das, R., Bradley, P. H., McCoy, A. J., Read, R. J., & Baker, D. A. (2007) · Nature · doi:10.1038/nature06249 · Cited by 317 · see citing works
High‐accuracy protein structure prediction in <scp>CASP14</scp>
Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26171 · Cited by 314 · see citing works
Self-citationThe Common Architecture of Cross-β Amyloid
Jahn, T. R., Makin, O. S., Morris, K. L., et al. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.09.039 · Cited by 305 · see citing works
Molecular architecture of the inner ring scaffold of the human nuclear pore complex
Kosiński, J., Mosalaganti, S., von Appen, A., Teimer, R., DiGuilio, A. L., Wan, W., Bui, K. H., Hagen, W. J. H., Briggs, J. A. G., Glavy, J. S., et al. (2016) · Science · doi:10.1126/science.aaf0643 · Cited by 303 · see citing works
The cytotoxic Staphylococcus aureus PSMα3 reveals a cross-α amyloid-like fibril
Tayeb-Fligelman, E., Tabachnikov, O., Moshe, A., Goldshmidt‐Tran, O., Sawaya, M. R., Coquelle, N., Colletier, J., & Landau, M. (2017) · Science · doi:10.1126/science.aaf4901 · Cited by 303 · see citing works
Self-citationMolecular Structures of Amyloid and Prion Fibrils: Consensus versus Controversy
Tycko, R., & Wickner, R. B. (2013) · Accounts of Chemical Research · doi:10.1021/ar300282r · Cited by 286 · see citing works
In-cell architecture of an actively transcribing-translating expressome
O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284 · see citing works
Melckebeke, H. V., Wasmer, C., Lange, A., Eiso, A. B., Loquet, A., Böckmann, A., & Meier, B. H. (2010) · Journal of the American Chemical Society · doi:10.1021/ja104213j · Cited by 283 · see citing works
LINUS: a hierarchic procedure to predict the fold of a protein
Srinivasan, R., & Rose, G. D. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340220202 · Cited by 266 · see citing works
X-ray studies of the structure of hair, wool, and related fibres.- I. General
Astbury, W. T., & Street, A. (1931) · Philosophical Transactions of the Royal Society of London Series A Containing Papers of a Mathematical or Physical Character · doi:10.1098/rsta.1932.0003 · Cited by 261 · see citing works
Molecular mechanisms for protein-encoded inheritance
Wiltzius, J. J. W., Landau, M., Nelson, R. A., Sawaya, M. R., Apostol, M. I., Goldschmidt, L., Soriaga, A. B., Cascio, D., Rajashankar, K. R., & Eisenberg, D. S. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1643 · Cited by 260 · see citing works
Self-citationCryo-EM structures of four polymorphic TDP-43 amyloid cores
Cao, Q., Boyer, D. R., Sawaya, M. R., Ge, P., & Eisenberg, D. S. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0248-4 · Cited by 253 · see citing works
Principles for Integrative Structural Biology Studies
Rout, M. P., & Šali, A. (2019) · Cell · doi:10.1016/j.cell.2019.05.016 · Cited by 249 · see citing works
Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation
Guenther, E. L., Cao, Q., Trinh, H., Lu, J., Sawaya, M. R., Cascio, D., Boyer, D. R., Rodríguez, J. A., Hughes, M. P., & Eisenberg, D. S. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0064-2 · Cited by 247 · see citing works
Molecular Structure of beta-Amyloid Fibrils in Alzheimer's Disease Brain Tissue.
Lu, J., Qiang, W., Yau, W., Schwieters, C. D., Meredith, S. C., & Tycko, R. (2013) · Cell · doi:10.2210/pdb2m4j/pdb · Cited by 246 · see citing works
Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation
Luo, F., Gui, X., Zhou, H., Gu, J., Li, Y., Liu, X., Zhao, M., Li, D., Li, X., & Liu, C. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0050-8 · Cited by 245 · see citing works
Wu, L., Yang, Y., Guo, X., Shu, X., Cai, Q., Shu, X., Li, B., Tao, R., Wu, C., Nikas, J. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17673-9 · Cited by 244 · see citing works
TWO HYDROGEN-BONDED SPIRAL CONFIGURATIONS OF THE POLYPEPTIDE CHAIN
Pauling, L. C., & Corey, R. B. (1950) · Journal of the American Chemical Society · doi:10.1021/ja01167a545 · Cited by 242 · see citing works
The structure of haemoglobin - IV. Sign determination by the isomorphous replacement method
Green, D. W., Ingram, V. M., & Perutz, M. F. (1954) · Proceedings of the Royal Society of London A Mathematical and Physical Sciences · doi:10.1098/rspa.1954.0203 · Cited by 239 · see citing works
Peptide dimer structure in an Aβ(1–42) fibril visualized with cryo-EM
Schmidt, M., Rohou, A. L., Lasker, K., Yadav, J. K., Schiene‐Fischer, C., Fändrich, M., & Grigorieff, N. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1503455112 · Cited by 219 · see citing works
Towards a Pharmacophore for Amyloid
Landau, M., Sawaya, M. R., Faull, K. F., Laganowsky, A. D., Jiang, L., Sievers, S. A., Liu, J., Barrio, J. R., & Eisenberg, D. S. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001080 · Cited by 209 · see citing works
Self-citationPolymorphic Fibril Formation by Residues 10–40 of the Alzheimer’s β-Amyloid Peptide
Paravastu, A. K., Petkova, A. T., & Tycko, R. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.076927 · Cited by 207 · see citing works
In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology
Asano, S. M., Engel, B. D., & Baumeister, W. P. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.09.030 · Cited by 198 · see citing works
Zhao, K., Lim, Y., Liu, Z., Long, H., Sun, Y., Hu, J., Zhao, C., Tao, Y., Zhang, X., Li, D., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1922741117 · Cited by 198 · see citing works
Conventions and workflows for using Situs
Wriggers, W. R. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911049791 · Cited by 197 · see citing works
Schmidt, M., Wiese, S., Adak, V., Engler, J., Agarwal, S., Fritz, G., Westermark, P., Zacharias, M., & Fändrich, M. (2019) · Nature Communications · doi:10.1038/s41467-019-13038-z · Cited by 194 · see citing works
Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS)
Graewert, M. A., & Svergun, D. I. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.06.007 · Cited by 190 · see citing works
Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila
Hervás, R., Rau, M., Park, Y., Zhang, W., Murzin, A. G., Fitzpatrick, J. A. J., Scheres, S. H. W., & Si, K. (2020) · Science · doi:10.1126/science.aba3526 · Cited by 189 · see citing works
Physical basis of amyloid fibril polymorphism
Close, W., Neumann, M., Schmidt, A., Hora, M., Annamalai, K., Schmidt, M., Reif, B., Schmidt, V., Grigorieff, N., & Fändrich, M. (2018) · Nature Communications · doi:10.1038/s41467-018-03164-5 · Cited by 183 · see citing works
De novo protein structure determination from near-atomic-resolution cryo-EM maps
Wang, R. Y., Kudryashev, M., Li, X., Egelman, E. H., Basler, M., Cheng, Y., Baker, D. A., & DiMaio, F. (2015) · Nature Methods · doi:10.1038/nmeth.3287 · Cited by 180 · see citing works
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 · see citing works
The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure
Boyer, D. R., Li, B., Sun, C., Fan, W., Zhou, K., Hughes, M. P., Sawaya, M. R., Jiang, L., & Eisenberg, D. S. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1917914117 · Cited by 179 · see citing works
Radamaker, L., Lin, Y.-H., Annamalai, K., Huhn, S., Hegenbart, U., Schönland, S. O., Fritz, G., Schmidt, M., & Fändrich, M. (2019) · Nature Communications · doi:10.1038/s41467-019-09032-0 · Cited by 178 · see citing works
An NMR View of Protein Dynamics in Health and Disease
Sekhar, A., & Kay, L. E. (2019) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-052118-115647 · Cited by 178 · see citing works
Microbial amyloids – functions and interactions within the host
Schwartz, K., & Boles, B. R. (2013) · Current Opinion in Microbiology · doi:10.1016/j.mib.2012.12.001 · Cited by 177 · see citing works
Structures of fibrils formed by α-synuclein hereditary disease mutant H50Q reveal new polymorphs
Boyer, D. R., Li, B., Sun, C., Fan, W., Sawaya, M. R., Jiang, L., & Eisenberg, D. S. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0322-y · Cited by 175 · see citing works
iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates
López‐Blanco, J. R., & Chacón, P. (2013) · Journal of Structural Biology · doi:10.1016/j.jsb.2013.08.010 · Cited by 173 · see citing works
The Three-Dimensional Structure of a Protein Molecule
Kendrew, J. C. (1961) · Scientific American · doi:10.1038/scientificamerican1261-96 · Cited by 166 · see citing works
The Human LL-37(17-29) antimicrobial peptide reveals a functional supramolecular structure
Engelberg, Y., & Landau, M. (2020) · Nature Communications · doi:10.1038/s41467-020-17736-x · Cited by 165 · see citing works
Self-citationSwuec, P., Lavatelli, F., Tasaki, M., Paissoni, C., Rognoni, P., Maritan, M., Brambilla, F., Milani, P., Mauri, P., Camilloni, C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09133-w · Cited by 162 · see citing works
Review: Electron Crystallography: Present Excitement, a Nod to the Past, Anticipating the Future
Glaeser, R. M. (1999) · Journal of Structural Biology · doi:10.1006/jsbi.1999.4172 · Cited by 155 · see citing works
Liu, Z., Vysotski, E. S., Vysotski, E. S., et al. (2000) · Protein Science · doi:10.1110/ps.9.11.2085 · Cited by 151 · see citing works
Liberta, F., Loerch, S., Rennegarbe, M., Schierhorn, A., Westermark, P., Westermark, G. T., Hazenberg, B. P. C., Grigorieff, N., Fändrich, M., & Schmidt, M. (2019) · Nature Communications · doi:10.1038/s41467-019-09033-z · Cited by 148 · see citing works
Sun, Y., Hou, S., Zhao, K., Long, H., Liu, Z., Gao, J., Zhang, Y., Su, X., Li, D., & Liu, C. (2020) · Cell Research · doi:10.1038/s41422-020-0299-4 · Cited by 146 · see citing works
High-throughput X-ray crystallography for drug discovery
Blundell, T. L., & Patel, S. (2004) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2004.04.007 · Cited by 141 · see citing works
The structure of a β2-microglobulin fibril suggests a molecular basis for its amyloid polymorphism
Iadanza, M. G., Silvers, R., Boardman, J., Smith, H. I., Karamanos, T. K., Debelouchina, G. T., Su, Y., Griffin, R. G., Ranson, N. A., & Radford, S. E. (2018) · Nature Communications · doi:10.1038/s41467-018-06761-6 · Cited by 141 · see citing works
Cryo-EM structure and inhibitor design of human IAPP (amylin) fibrils
Cao, Q., Boyer, D. R., Sawaya, M. R., Ge, P., & Eisenberg, D. S. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0435-3 · Cited by 138 · see citing works
Ni, X., McGlinchey, R. P., Jiang, J., & Lee, J. C. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.001 · Cited by 136 · see citing works
The Specular Reflection of X-rays.
Bragg, W. L. (1912) · Nature · doi:10.1038/090410b0 · Cited by 132 · see citing works
Taylor, G. L. (2003) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444903017815 · Cited by 127 · see citing works
Deep learning techniques have significantly impacted protein structure prediction and protein design
Pearce, R., & Zhang, Y. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.01.007 · Cited by 127 · see citing works
Sequence‐similar, structure‐dissimilar protein pairs in the PDB
Kosloff, M., & Kolodny, R. (2008) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21770 · Cited by 124 · see citing works
Self-citationExtreme amyloid polymorphism in Staphylococcus aureus virulent PSMα peptides
Salinas, N., Colletier, J., Moshe, A., & Landau, M. (2018) · Nature Communications · doi:10.1038/s41467-018-05490-0 · Cited by 124 · see citing works
Self-citationAtomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2
Guenther, E. L., Ge, P., Trinh, H., Sawaya, M. R., Cascio, D., Boyer, D. R., Gonen, T., Zhou, Z. H., & Eisenberg, D. S. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0045-5 · Cited by 121 · see citing works
An introduction to molecular replacement
Evans, P., & McCoy, A. J. (2007) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444907051554 · Cited by 114 · see citing works
The crystal structure of the alums
Lipson, H., & Beevers, C. A. (1935) · Proceedings of the Royal Society of London A Mathematical and Physical Sciences · doi:10.1098/rspa.1935.0040 · Cited by 113 · see citing works
Soragni, A., Yousefi, S., Stoeckle, C., Soriaga, A. B., Sawaya, M. R., Kozlowski, E., Schmid, I., Radonjic‐Hoesli, S., Boutet, S., Williams, G. J., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.026 · Cited by 111 · see citing works
Perov, S., Lidor, O., Salinas, N., Golan, N., Tayeb-Fligelman, E., Deshmukh, M. G., Willbold, D., & Landau, M. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007978 · Cited by 109 · see citing works
Self-citationCryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid
Lu, J., Cao, Q., Hughes, M. P., Sawaya, M. R., Boyer, D. R., Cascio, D., & Eisenberg, D. S. (2020) · Nature Communications · doi:10.1038/s41467-020-17905-y · Cited by 109 · see citing works
Molecular structure of the intact bacterial flagellar basal body
Johnson, S., Furlong, E., Deme, J. C., Nord, A. L., Caesar, J. J. E., Chevance, F. F. V., Berry, R. M., Hughes, K. T., & Lea, S. M. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00895-y · Cited by 109 · see citing works
Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS)
Gräwert, T., & Svergun, D. I. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.01.030 · Cited by 108 · see citing works
(2018) · International Conference on Learning Representations · Cited by 92 · see citing works
NMR Spectroscopy of Soluble Protein Complexes at One Mega‐Dalton and Beyond
Mainz, A., Religa, T. L., Sprangers, R., et al. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201301215 · Cited by 91 · see citing works
Cryo-electron microscopy analysis of small membrane proteins
Nygaard, R., Kim, J., & Mancia, F. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.05.009 · Cited by 90 · see citing works
Integrative Modelling of Biomolecular Complexes
Koukos, P. I., & Bonvin, A. M. J. J. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.11.009 · Cited by 89 · see citing works
AlphaFold and the amyloid landscape
Pinheiro, F., Santos, J., & Ventura, S. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167059 · Cited by 88 · see citing works
A Modified Differential Refractometer
KŐRÖSY, F. (1954) · Nature · doi:10.1038/174269b0 · Cited by 86 · see citing works
Structure of Optically Active Compounds in the Solid State
Bijvoet, J. M. (1954) · Nature · doi:10.1038/173888a0 · Cited by 82 · see citing works
Staphylococcus aureus PSMα3 Cross-α Fibril Polymorphism and Determinants of Cytotoxicity
Tayeb-Fligelman, E., Salinas, N., Tabachnikov, O., & Landau, M. (2020) · Structure · doi:10.1016/j.str.2019.12.006 · Cited by 82 · see citing works
Self-citationIntroduction to Proteins: Structure, Function, and Motion
Kessel, A., & Ben‐Tal, N. (2010) · Thammasat University Digital Collections · Cited by 78 · see citing works
Self-citationBurra, P. V. L. S., Zhang, Y., Godzik, A., & Stec, B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812152106 · Cited by 78 · see citing works
Architecture of the yeast Elongator complex
Daudén, M. I., Kosiński, J., Kolaj‐Robin, O., Desfosses, A., Ori, A., Faux, C., Hoffmann, N. A., Onuma, O. F., Breunig, K. D., Beck, M., et al. (2016) · EMBO Reports · doi:10.15252/embr.201643353 · Cited by 77 · see citing works
The Southeast Collaboratory for Structural Genomics: A High-Throughput Gene to Structure Factory
Adams, M. W. W., Dailey, H. A., DeLucas, L. J., et al. (2003) · Accounts of Chemical Research · doi:10.1021/ar0101382 · Cited by 77 · see citing works
High‐accuracy protein structures by combining machine‐learning with physics‐based refinement
Heo, L., & Feig, M. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25847 · Cited by 76 · see citing works
The three-dimensional structure of human β-endorphin amyloid fibrils
Seuring, C., Verasdonck, J., Gath, J., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-00515-z · Cited by 74 · see citing works
Isomorphous replacement and phase determination in non-centrosymmetric space groups
Perutz, M. F. (1956) · Acta Crystallographica · doi:10.1107/s0365110x56002485 · Cited by 73 · see citing works
An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity
Debruycker, V., Hutchin, A., Masureel, M., Ficici, E., Martens, C., Legrand, P., Stein, R. A., Mchaourab, H. S., Faraldo-Gómez, J. D., Remaut, H., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0464-y · Cited by 69 · see citing works
The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid
Salinas, N., Tayeb-Fligelman, E., Sammito, M. D., Bloch, D. N., Jelinek, R., Noy, D., Usón, I., & Landau, M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2014442118 · Cited by 66 · see citing works
Self-citationFold modulating function: bacterial toxins to functional amyloids
Syed, A. K., & Boles, B. R. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00401 · Cited by 65 · see citing works
Microbial manipulation of the amyloid fold
DePas, W. H., & Chapman, M. R. (2012) · Research in Microbiology · doi:10.1016/j.resmic.2012.10.009 · Cited by 64 · see citing works
Segmental Polymorphism in a Functional Amyloid
Hu, K., McGlinchey, R. P., Wickner, R. B., et al. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.09.051 · Cited by 63 · see citing works
Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit
van Zundert, G. C. P., & Bonvin, A. M. J. J. (2015) · AIMS Biophysics · doi:10.3934/biophy.2015.2.73 · Cited by 62 · see citing works
Kummer, M. P., Maruyama, H., Hülsmann, C., Baches, S., Weggen, S., & Koo, E. H. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m808904200 · Cited by 60 · see citing works
Ab initio solution of macromolecular crystal structures without direct methods
McCoy, A. J., Oeffner, R. D., Wrobel, A. G., Ojala, J. R. M., Tryggvason, K., Lohkamp, B., & Read, R. J. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1701640114 · Cited by 60 · see citing works
ChSeq : A database of chameleon sequences
Li, W., Kinch, L. N., Karplus, P. A., & Grishin, N. V. (2015) · Protein Science · doi:10.1002/pro.2689 · Cited by 59 · see citing works
Unravelling molecular complexity in structural cell biology.
Pfeffer, S., & Mahamid, J. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.08.009 · Cited by 59 · see citing works
Modelling structures in cryo-EM maps
Malhotra, S., Träger, S., Peraro, M. D., & Topf, M. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.05.024 · Cited by 58 · see citing works
Biophysical Techniques in Structural Biology
Dobson, C. M. (2019) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-111947 · Cited by 56 · see citing works
Introduction to proteins—structure, function, and motion
Martz, E. (2012) · Biochemistry and Molecular Biology Education · doi:10.1002/bmb.20603 · Cited by 54 · see citing works
Functional Amyloids in Reproduction
Hewetson, A., Do, H. Q., Myers, C., et al. (2017) · Biomolecules · doi:10.3390/biom7030046 · Cited by 54 · see citing works
Integrative structural modeling of macromolecular complexes using Assembline
Rantos, V., Karius, K., & Kosiński, J. (2021) · Nature Protocols · doi:10.1038/s41596-021-00640-z · Cited by 52 · see citing works
Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
Flower, T. G., & Hurley, J. H. (2021) · Protein Science · doi:10.1002/pro.4050 · Cited by 49 · see citing works
Functional and pathological amyloid structures in the eyes of 2020 cryo-EM
Ragonis‐Bachar, P., & Landau, M. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.01.006 · Cited by 49 · see citing works
Self-citationLauer, J. L., Segeletz, S., Cezanne, A., Guaitoli, G., Raimondi, F., Gentzel, M., Alva, V., Habeck, M., Kalaidzidis, Y. L., Ueffing, M., et al. (2019) · eLife · doi:10.7554/elife.46302 · Cited by 45 · see citing works
Self-citationViswanath, S., Bonomi, M., Kim, S. J., Klenchin, V. A., Taylor, K. C., Yabut, K. C. B., Umbreit, N. T., Epps, H. A. V., Meehl, J. B., Jones, M. H., et al. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e17-06-0397 · Cited by 44 · see citing works
Towards high-throughput in situ structural biology using electron cryotomography
Böhning, J., & Bharat, T. A. M. (2020) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2020.05.010 · Cited by 44 · see citing works
ON SOME GENERAL PROPERTIES OF PROTEINS
Anson, M. L., & Mirsky, A. E. (1925) · The Journal of General Physiology · doi:10.1085/jgp.9.2.169 · Cited by 40 · see citing works
LX.The crystal structure of some of the alums
Cork, J. M. (1927) · The London Edinburgh and Dublin Philosophical Magazine and Journal of Science · doi:10.1080/14786441008564371 · Cited by 38 · see citing works
Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes
Bernal, I., Börnicke, J., Heidemann, J., et al. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.004 · Cited by 35 · see citing works
CoDNaS: a database of conformational diversity in the native state of proteins
Monzón, A. M., Juritz, E., Fornasari, M. S., & Parisi, G. D. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt405 · Cited by 30 · see citing works
Ghosh, U., Yau, W., & Tycko, R. (2018) · Chemical Communications · doi:10.1039/c8cc01967c · Cited by 29 · see citing works
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP
del Alamo, D., Govaerts, C., & Mchaourab, H. S. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26138 · Cited by 29 · see citing works
PCDB: a database of protein conformational diversity
Juritz, E., Fernández-Alberti, S., & Parisi, G. D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1181 · Cited by 28 · see citing works
X-ray analysis and application of fourier series methods to molecular structures
ROBERTSON, J. M. (1937) · Reports on Progress in Physics · doi:10.1088/0034-4885/4/1/324 · Cited by 19 · see citing works
Mapping Local Conformational Landscapes of Proteins in Solution
ElGamacy, M., Riss, M., Zhu, H., et al. (2019) · Structure · doi:10.1016/j.str.2019.03.005 · Cited by 18 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Demis Hassabis, Brief update on some exciting progress on #AlphaFold! We've been heads down working flat out on our full methods paper (currently under review) with accompanying open source code and on providing broad free access to AlphaFold for the scientific community. More very soon! https://t.co/uP7uzgGMSf, @demishassabis. (2021). https://twitter.com/demishassabis/status/1405922 961710854144 (accessed June 23, 2021).
Cited by
Sorted by citations
AI-based structure prediction empowers integrative structural analysis of human nuclear pores
Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., Buczak, K., Schmidt, F. H., Margiotta, E., Mackmull, M.-T., et al. (2022) · Science · doi:10.1126/science.abm9506 · Cited by 355 · see citing works
Lindorff-Larsen, K., & Kragelund, B. B. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167196 · Cited by 85 · see citing works
Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac118 · Cited by 32 · see citing works
Varadi, M., Bordin, N., Orengo, C., & Velankar, S. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102543 · Cited by 29 · see citing works
- Authors
- Masrati, G., Landau, M., Ben-Tal, N., Lupas, A., Kosloff, M., & Kosinski, J.
- Affiliations
- Tel Aviv University (IL)
- Technion – Israel Institute of Technology (IL)
- Max Planck Institute for Developmental Biology (DE)
- University of Haifa (IL)
- Corresponding author
- Lupas, Andrei
- Kosloff, Mickey
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2021-10
- Volume
- 433
- Issue
- 20
- Pages
- 167127
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W3181374387
- Cited by
- 53
- References
- 213
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 8 · 2023: 9 · 2022: 21 · 2021: 7
- FWCI
- 1.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Desy Publications Database (Deutsches Elektronen-Synchrotron DESY) (submittedVersion, other-oa)
- Funders
- Max-Planck-Gesellschaft
- Tel Aviv University
- Canadian Institutes of Health Research
- BMBF Berlin
- International Development Research Centre
- Azrieli Foundation (3512/19)
- Israel Science Foundation
- Bundesministerium für Bildung und Forschung (FKZ 031L0100)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- integrative structural biology, protein structure prediction, AlphaFold2, macromolecular structure determination, protein complexes, structural polymorphism, structure-function relationship
- MeSH terms
- Animals, Humans, Models, Molecular, Protein Conformation, Proteins, Crystallography, X-Ray, Nuclear Magnetic Resonance, Biomolecular
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