AlphaFold and the amyloid landscape
Abstract
Protein aggregation is a widespread phenomenon with important implications in many scientific areas. Although amyloid formation is typically considered as detrimental, functional amyloids that perform physiological roles have been identified in all kingdoms of life. Despite their functional and pathological relevance, the structural details of the majority of molecular species involved in the amyloidogenic process remains elusive. Here, we explore the application of AlphaFold, a highly accurate protein structure predictor, in the field of protein aggregation. While we envision a straightforward application of AlphaFold in assisting the design of globular proteins with improved solubility for biomedical and industrial purposes, the use of this algorithm for predicting the structure of aggregated species seems far from trivial. First, in amyloid diseases, the presence of multiple amyloid polymorphs and the heterogeneity of aggregation intermediates challenges the "one sequence, one structure" paradigm, inherent to sequence-based predictions. Second, aberrant aggregation is not the subject of positive selective pressure, precluding the use of evolutionary-based approaches, which are the core of the AlphaFold pipeline. Instead, amyloid polymorphism seems to be constrained by the need for a defined structure-activity relationship in functional amyloids. They may thus provide a starting point for the application of AlphaFold in the amyloid landscape.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
The AF2 model of the beta-endorphin amyloid fiber is incorrect compared with its solid-state NMR structure.
“the incorrect AF2 model of the beta-endorphin amyloid fiber relative to its experimental solid-state NMR structure58”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [58]
Cites
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
Improved protein structure prediction using potentials from deep learning
Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T., Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., et al. (2020) · Nature · doi:10.1038/s41586-019-1923-7 · Cited by 3,378 · see citing works
Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein
Hartl, F. U., & Hayer-Hartl, M. K. (2002) · Science · doi:10.1126/science.1068408 · Cited by 3,335 · see citing works
The Energy Landscapes and Motions of Proteins
Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991) · Science · doi:10.1126/science.1749933 · Cited by 3,250 · see citing works
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
Wright, P. E., & Dyson, H. J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3110 · Cited by 2,968 · see citing works
Protein Misfolding, Amyloid Formation, and Human Disease: A Summary of Progress Over the Last Decade
Chiti, F., & Dobson, C. M. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-045115 · Cited by 2,629 · see citing works
Goedert, M., Spillantini, M. G., Jakes, R., Rutherford, D., & Crowther, R. A. (1989) · Neuron · doi:10.1016/0896-6273(89)90210-9 · Cited by 2,492 · see citing works
Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases
Bucciantini, M., Giannoni, E., Chiti, F., Baroni, F., Formigli, L., Zurdo, J., Taddei, N., Ramponi, G., Dobson, C. M., & Stefani, M. (2002) · Nature · doi:10.1038/416507a · Cited by 2,434 · see citing works
Atomic structures of amyloid cross-β spines reveal varied steric zippers
Sawaya, M. R., Sambashivan, S., Nelson, R. A., Ivanova, M. I., Sievers, S. A., Apostol, M. I., Thompson, M. J., Balbirnie, M., Wiltzius, J. J. W., McFarlane, H. T., et al. (2007) · Nature · doi:10.1038/nature05695 · Cited by 2,279 · 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
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
Fernández‐Escamilla, A. M., Rousseau, F., Schymkowitz, J. W. H., & Serrano, L. G. (2004) · Nature Biotechnology · doi:10.1038/nbt1012 · Cited by 1,663 · see citing works
In vivo demonstration that α-synuclein oligomers are toxic
Winner, B., Jappelli, R., Maji, S. K., Desplats, P., Boyer, L. F., Aigner, S., Hetzer, C., Loher, T., Vilar, M., Campioni, S., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100976108 · Cited by 1,487 · see citing works
Architecture of the human interactome defines protein communities and disease networks
Huttlin, E. L., Bruckner, R. J., Paulo, J. A., Cannon, J. R., Ting, L., Baltier, K., Colby, G., Gebreab, F., Gygi, M. P., Parzen, H., et al. (2017) · Nature · doi:10.1038/nature22366 · Cited by 1,437 · 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
EGCG redirects amyloidogenic polypeptides into unstructured, off-pathway oligomers
Ehrnhoefer, D. E., Bieschke, J., Boeddrich, A., Herbst, M., Masino, L., Lurz, R., Engemann, S., Pastore, A., & Wanker, E. (2008) · Nature Structural &Molecular Biology · doi:10.1038/nsmb.1437 · Cited by 1,424 · see citing works
Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils
Ahmed, M., Davis, J., Aucoin, D., Sato, T., Ahuja, S., Aimoto, S., Elliott, J. I., Van Nostrand, W. E., & Smith, S. O. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1799 · Cited by 1,111 · see citing works
Jeffery, C. J. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01335-8 · Cited by 1,084 · see citing works
Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions
Tompa, P., & Fuxreiter, M. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.10.003 · Cited by 1,080 · see citing works
Eliezer, D., Kutluay, E., Bussell, R., & Browne, G. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4538 · Cited by 1,077 · see citing works
Mechanism of coupled folding and binding of an intrinsically disordered protein
Sugase, K., Dyson, H. J., & Wright, P. E. (2007) · Nature · doi:10.1038/nature05858 · Cited by 1,040 · see citing works
Wright, P. E., & Dyson, H. J. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.12.003 · Cited by 1,012 · see citing works
Das, R. K., & Pappu, R. V. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1304749110 · Cited by 1,008 · see citing works
Amyloid Fibrils of the HET-s(218–289) Prion Form a β Solenoid with a Triangular Hydrophobic Core
Wasmer, C., Lange, A., Melckebeke, H. V., Siemer, A. B., Riek, R., & Meier, B. H. (2008) · Science · doi:10.1126/science.1151839 · Cited by 998 · see citing works
What does it mean to be natively unfolded?
Uversky, V. N. (2002) · European Journal of Biochemistry · doi:10.1046/j.0014-2956.2001.02649.x · Cited by 985 · see citing works
Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein
Tuttle, M. D., Comellas, G., Nieuwkoop, A. J., Covell, D. J., Berthold, D. A., Kloepper, K. D., Courtney, J. M., Kim, J. K., Barclay, A. M., Kendall, A. K., et al. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3194 · Cited by 951 · see citing works
Techniques to study amyloid fibril formation in vitro
NILSSON, M. (2004) · Methods · doi:10.1016/j.ymeth.2004.03.012 · Cited by 948 · 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
Goedert, M., & Jakes, R. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07870.x · Cited by 929 · see citing works
Direct Observation of the Interconversion of Normal and Toxic Forms of α-Synuclein
Cremades, N., Cohen, S. I. A., Deas, E., Abramov, A. Y., Chen, A. Y., Orte, Á., Sandal, M., Clarke, R. W., Dunne, P., Aprile, F. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.037 · Cited by 901 · see citing works
Structural and functional characterization of two alpha-synuclein strains
Bousset, L., Pieri, L., Ruiz-Arlandis, G., Gath, J., Jensen, P. H., Habenstein, B., Madiona, K., Oliéric, V., Böckmann, A., Meier, B. H., et al. (2013) · Nature Communications · doi:10.1038/ncomms3575 · Cited by 890 · see citing works
Correlated mutations and residue contacts in proteins
Göbel, U., Sander, C., Schneider, R., & Valencia, A. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180402 · Cited by 863 · see citing works
Bernstein, S. L., Dupuis, N., Lazo, N., Wyttenbach, T., Condron, M., Bitan, G., Teplow, D., Shea, J., Ruotolo, B., Robinson, C., et al. (2009) · Nature Chemistry · doi:10.1038/nchem.247 · Cited by 847 · 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
Bertoncini, C. W., Jung, Y., Fernández, C. O., Hoyer, W., Griesinger, C., Jovin, T. M., & Zweckstetter, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407146102 · Cited by 781 · 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
Kayed, R., Head, E., Sarsoza, F., Saing, T., Cotman, C. W., Necula, M., Margol, L., Wu, J., Breydo, L., Thompson, J. L., et al. (2007) · Molecular Neurodegeneration · doi:10.1186/1750-1326-2-18 · Cited by 773 · see citing works
Jones, D. T., Buchan, D. W. A., Cozzetto, D., & Pontil, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr638 · Cited by 760 · see citing works
Protein aggregation and bioprocessing
Cromwell, M. E. M., Hilario, E., & Jacobson, F. (2006) · The AAPS Journal · doi:10.1208/aapsj080366 · Cited by 758 · see citing works
Comparison of kindreds with parkinsonism and α‐synuclein genomic multiplications
Farrer, M. J., Kachergus, J. M., Forno, L. S., Lincoln, S., Wang, D., Hulihan, M., Maraganore, D. M., Gwinn, K. A., Wszołek, Z. K., Dickson, D. W., et al. (2004) · Annals of Neurology · doi:10.1002/ana.10846 · Cited by 699 · see citing works
Kirkitadze, M. D., Condron, M. M., & Teplow, D. B. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4970 · Cited by 684 · see citing works
Distinct α-Synuclein Strains Differentially Promote Tau Inclusions in Neurons
Guo, J. L., Covell, D. J., Daniels, J. P., Iba, M., Stieber, A., Zhang, B., Riddle, D. M., Kwong, L. K., Xu, Y., Trojanowski, J. Q., et al. (2013) · Cell · doi:10.1016/j.cell.2013.05.057 · Cited by 680 · see citing works
Structural basis of membrane disruption and cellular toxicity by α-synuclein oligomers
Fusco, G., Chen, S. W., Williamson, P. T. F., Cascella, R., Perni, M., Jarvis, J. A., Cecchi, C., Vendruscolo, M., Chiti, F., Cremades, N., et al. (2017) · Science · doi:10.1126/science.aan6160 · Cited by 665 · see citing works
Intrinsic protein disorder in complete genomes.
Dunker, A. K., Zoran Obradovic, A., Romero, P. R., Garner, E. C., & Brown, C. J. (2000) · PubMed · Cited by 661 · see citing works
Barrow, C. J., Yasuda, A., Kenny, P. T. M., & Zagorski, M. G. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90106-t · Cited by 636 · see citing works
Propagation of Tau aggregates and neurodegeneration
Goedert, M., Eisenberg, D. S., & Crowther, R. A. (2017) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-072116-031153 · Cited by 632 · see citing works
Intrinsically disordered proteins: a 10-year recap
Tompa, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.08.004 · Cited by 624 · 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
Design of therapeutic proteins with enhanced stability
Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., & Trout, B. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904191106 · Cited by 597 · see citing works
Intrinsically disordered proteins: regulation and disease
Babu, M. M., van der Lee, R., de Groot, N. S., & Gsponer, J. A. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.011 · Cited by 597 · see citing works
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners
Oldfield, C. J., Meng, J., Yang, J. Y., Yang, M. Q., Uversky, V. N., & Dunker, A. K. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-s1-s1 · Cited by 594 · see citing works
The physical basis of how prion conformations determine strain phenotypes
Tanaka, M., Collins, S. R., Toyama, B. H., & Weissman, J. S. (2006) · Nature · doi:10.1038/nature04922 · Cited by 589 · see citing works
The protein trinity—linking function and disorder
Dunker, A. K., & Obradovic, Z. (2001) · Nature Biotechnology · doi:10.1038/nbt0901-805 · Cited by 581 · see citing works
Schweers, O., Schönbrunn, E., Marx, A., & Mandelkow�, E. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)51080-8 · Cited by 569 · see citing works
Half a century of amyloids: past, present and future
Ke, P. C., Zhou, R., Serpell, L. C., Riek, R., Knowles, T. P. J., Lashuel, H. A., Gazit, E., Hamley, I. W., Davis, T. P., Fändrich, M., et al. (2020) · Chemical Society Reviews · doi:10.1039/c9cs00199a · Cited by 567 · see citing works
Atomic View of a Toxic Amyloid Small Oligomer
Laganowsky, A. D., Liu, C., Sawaya, M. R., Whitelegge, J. P., Park, J., Zhao, M., Pensalfini, A., Soriaga, A. B., Landau, M., Teng, P. K., et al. (2012) · Science · doi:10.1126/science.1213151 · Cited by 564 · see citing works
The role of structural disorder in the function of RNA and protein chaperones
Tompa, P., & Csermely, P. (2004) · The FASEB Journal · doi:10.1096/fj.04-1584rev · Cited by 555 · see citing works
Inhibition of MDM2-mediated p53 Ubiquitination and Degradation by Ribosomal Protein L5
Dai, M., & Lu, H. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m403722200 · Cited by 536 · see citing works
Critical assessment of methods of protein structure prediction (CASP)—Round XIII
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2019) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25823 · Cited by 506 · see citing works
Uversky, V. N. (2003) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2003.10506918 · 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
Roey, K. V., Uyar, B., Weatheritt, R. J., Dinkel, H., Seiler, M., Budd, A., Gibson, T. J., & Davey, N. E. (2014) · Chemical Reviews · doi:10.1021/cr400585q · Cited by 496 · see citing works
The CamSol method of rational design of protein mutants with enhanced solubility
Sormanni, P., Aprile, F. A., & Vendruscolo, M. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.09.026 · Cited by 494 · see citing works
Chen, S. W., Drakulić, S., Deas, E., Ouberai, M. M., Aprile, F. A., Arranz, R., Ness, S., Roodveldt, C., Guilliams, T., Genst, E. D., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421204112 · Cited by 471 · see citing works
Structural disorder throws new light on moonlighting
Tompa, P., Szász, C., & Buday, L. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.07.008 · Cited by 468 · see citing works
Strong underwater adhesives made by self-assembling multi-protein nanofibres
Zhong, C., Gurry, T., Cheng, A. A., Downey, J., Deng, Z., Stultz, C. M., & Lu, T. K. (2014) · Nature Nanotechnology · doi:10.1038/nnano.2014.199 · Cited by 446 · see citing works
Correlation of structural elements and infectivity of the HET-s prion
Ritter, C., Maddelein, M., Siemer, A. B., Lührs, T., Ernst, M., Meier, B. H., Saupe, S. J., & Riek, R. (2005) · Nature · doi:10.1038/nature03793 · Cited by 437 · see citing works
Folding versus aggregation: Polypeptide conformations on competing pathways
Jahn, T. R., & Radford, S. E. (2007) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2007.05.015 · Cited by 428 · see citing works
Neuropathology underlying clinical variability in patients with synucleinopathies
Halliday, G. M., Holton, J. L., Révész, T., & Dickson, D. W. (2011) · Acta Neuropathologica · doi:10.1007/s00401-011-0852-9 · Cited by 426 · see citing works
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 · 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
Structure of an Intermediate State in Protein Folding and Aggregation
Neudecker, P., Robustelli, P., Cavalli, A., Walsh, P., Lundström, P., Zarrine‐Afsar, A., Sharpe, S. J., Vendruscolo, M., & Kay, L. E. (2012) · Science · doi:10.1126/science.1214203 · Cited by 399 · see citing works
Reixach, N., Deechongkit, S., Jiang, X., Kelly, J. W., & Buxbaum, J. N. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400062101 · Cited by 392 · see citing works
Annular Protofibrils Are a Structurally and Functionally Distinct Type of Amyloid Oligomer
Kayed, R., Pensalfini, A., Margol, L., Sokolov, Y., Sarsoza, F. M., Head, E., Hall, J. E., & Glabe, C. G. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m808591200 · Cited by 348 · see citing works
Strategies for the assessment of protein aggregates in pharmaceutical biotech product development
den Engelsman, J., Garidel, P., Smulders, R., Koll, H., Smith, B., Bassarab, S., Seidl, A., Hainzl, O., & Jiskoot, W. (2011) · Pharmaceutical Research · doi:10.1007/s11095-010-0297-1 · Cited by 348 · see citing works
Competing Pathways Determine Fibril Morphology in the Self-assembly of β2-Microglobulin into Amyloid
Gosal, W. S., Morten, I. J., Hewitt, E. W., Smith, D. A., Thomson, N. H., & Radford, S. E. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.06.040 · Cited by 343 · see citing works
Transthyretin Aggregation under Partially Denaturing Conditions Is a Downhill Polymerization
Hurshman, A. R., White, J. T., Powers, E. T., & Kelly, J. W. (2004) · Biochemistry · doi:10.1021/bi049621l · Cited by 340 · 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
Conformational Abs recognizing a generic amyloid fibril epitope
O’Nuallain, B., & Wetzel, R. B. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.022662599 · Cited by 331 · see citing works
Insights into prion strains and neurotoxicity
Aguzzi, A., Heikenwälder, M. F., & Polymenidou, M. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2204 · Cited by 327 · see citing works
Critical assessment of methods of protein structure prediction (CASP)—Round XII
Moult, J., Fidelis, K. A., Kryshtafovych, A., Schwede, T. F., & Tramontano, A. L. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25415 · Cited by 327 · see citing works
Protein aggregation and its impact on product quality
Roberts, C. J. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.08.001 · Cited by 318 · see citing works
Elam, J. S., Taylor, A. B., Strange, R. W., Antonyuk, S. V., Doucette, P. A., Rodriguez, J. A., Hasnain, S. S., Hayward, L. J., Valentine, J. S., Yeates, T. O., et al. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb935 · Cited by 317 · see citing works
Partially Unfolded States of β2-Microglobulin and Amyloid Formation in Vitro
McParland, V. J., Kad, N. M., Kalverda, A. P., Brown, A., Kirwin-Jones, P., Hunter, M., Sunde, M., & Radford, S. E. (2000) · Biochemistry · doi:10.1021/bi000276j · Cited by 309 · see citing works
Amyloid formation under physiological conditions proceeds via a native-like folding intermediate
Jahn, T. R., Parker, M. J., Homans, S. W., & Radford, S. E. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1058 · Cited by 306 · see citing works
Aβ(1-40) Fibril Polymorphism Implies Diverse Interaction Patterns in Amyloid Fibrils
Meinhardt, J., Sachse, C., Hortschansky, P., Grigorieff, N., & Fändrich, M. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.11.005 · Cited by 300 · see citing works
A Diversity of Assembly Mechanisms of a Generic Amyloid Fold
Eichner, T., & Radford, S. E. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.05.012 · Cited by 293 · see citing works
Wacker, J. L., Zareie, M. H., Fong, H. K., Sarıkaya, M., & Muchowski, P. J. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb860 · Cited by 284 · see citing works
Atomic‐Resolution Three‐Dimensional Structure of Amyloid β Fibrils Bearing the Osaka Mutation
Schütz, A. K., Vagt, T., Huber, M., Ovchinnikova, O. Y., Cadalbert, R., Wall, J. S., Güntert, P., Böckmann, A., Glockshuber, R., & Meier, B. H. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201408598 · Cited by 282 · see citing works
Arosio, P., Michaels, T. C. T., Linse, S. S., Månsson, C., Emanuelsson, C. S., Presto, J., Johansson, J., Vendruscolo, M., Dobson, C. M., & Knowles, T. P. J. (2016) · Nature Communications · doi:10.1038/ncomms10948 · Cited by 259 · see citing works
Intrinsically Disordered Segments Affect Protein Half-Life in the Cell and during Evolution
van der Lee, R., Lang, B., Kruse, K., Gsponer, J. A., de Groot, N. S., Huynen, M. A., Matouschek, A. T., Fuxreiter, M., & Babu, M. M. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.055 · Cited by 229 · see citing works
Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme
Canet, D., Last, A. M., Tito, P., et al. (2002) · Nature Structural Biology · doi:10.1038/nsb768 · Cited by 228 · see citing works
Specific Pathological Tau Protein Variants Characterize Pickʼs Disease
Delacourte, A., Robitaille, Y., Sergeant, N., Buée, L., Hof, P. R., Wattez, A., Laroche-Cholette, A., Mathieu, J., Chagnon, P., & Gauvreau, D. (1996) · Journal of Neuropathology & Experimental Neurology · doi:10.1097/00005072-199602000-00004 · Cited by 224 · see citing works
Ghosh, D., Singh, P. K., Sahay, S., Jha, N. N., Jacob, R. S., Sen, S., Kumar, A., Riek, R., & Maji, S. K. (2015) · Scientific Reports · doi:10.1038/srep09228 · Cited by 213 · see citing works
Deep‐learning contact‐map guided protein structure prediction in CASP13
Zheng, W., Li, Y., Zhang, C., Pearce, R., Mortuza, S. M., & Zhang, Y. (2019) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25792 · Cited by 208 · see citing works
Tauopathies as clinicopathological entities
Irwin, D. J. (2015) · Parkinsonism & Related Disorders · doi:10.1016/j.parkreldis.2015.09.020 · Cited by 199 · see citing works
A mechanistic model of tau amyloid aggregation based on direct observation of oligomers
Shammas, S. L., Garcia, G. A., Kumar, S., Kjærgaard, M., Horrocks, M. H., Shivji, N., Mandelkow, E., Knowles, T. P. J., Mandelkow�, E., & Klenerman, D. (2015) · Nature Communications · doi:10.1038/ncomms8025 · Cited by 195 · see citing works
Lindberg, M. J., Tibell, L. A. E., & Oliveberg, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.262527099 · Cited by 194 · see citing works
Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility
Kuriata, A., Iglesias, V., Pujols, J., Kurciński, M., Kmiecik, S., & Ventura, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz321 · Cited by 190 · see citing works
Self-citationAmyloid structures: much more than just a cross-β fold
Gallardo, R. U., Ranson, N. A., & Radford, S. E. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.09.001 · Cited by 189 · see citing works
Amyloidogenesis of Natively Unfolded Proteins
Uversky, V. N. (2008) · Current Alzheimer Research · doi:10.2174/156720508784533312 · Cited by 187 · see citing works
Jones, D. T., & Kandathil, S. M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty341 · Cited by 184 · 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
Distinct synthetic Aβ prion strains producing different amyloid deposits in bigenic mice
Stöhr, J., Condello, C., Watts, J. C., Bloch, L., Oehler, A., Nick, M., DeArmond, S. J., Giles, K., DeGrado, W. F., & Prusiner, S. B. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1408968111 · Cited by 176 · see citing works
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes
Levy, E. D., De, S., & Teichmann, S. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1209312109 · Cited by 175 · see citing works
GroEL-Mediated Protein Folding: Making the Impossible, Possible
Lin, Z., & Rye, H. S. (2006) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230600760382 · Cited by 173 · see citing works
Triggers of Full-Length Tau Aggregation: A Role for Partially Folded Intermediates
Chirita, C. N., Congdon, E. E., Yin, H., & Kuret, J. (2005) · Biochemistry · doi:10.1021/bi0500123 · Cited by 166 · see citing works
The Amyloid Phenomenon and Its Significance in Biology and MedicinePreprint
Dobson, C. M., Knowles, T. P. J., & Vendruscolo, M. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a033878 · Cited by 166 · see citing works
Pechmann, S., Levy, E. D., Tartaglia, G. G., & Vendruscolo, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812414106 · Cited by 159 · see citing works
Li, J., Uversky, V. N., & Fink, A. L. (2002) · NeuroToxicology · doi:10.1016/s0161-813x(02)00066-9 · Cited by 158 · see citing works
The Effect of Disease-associated Mutations on the Folding Pathway of Human Prion Protein
Apetri, A. C., Surewicz, K. A., & Surewicz, W. K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m313581200 · Cited by 155 · see citing works
Smith, D. P., Radford, S. E., & Ashcroft, A. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913046107 · Cited by 152 · see citing works
Prediction and Reduction of the Aggregation of Monoclonal Antibodies
van der Kant, R., Karow‐Zwick, A. R., Durme, J. V., Blech, M., Gallardo, R. U., Seeliger, D., Aßfalg, K., Baatsen, P., Compernolle, G., Gils, A., et al. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.03.014 · Cited by 149 · see citing works
Smith, A. M., Jahn, T. R., Ashcroft, A. E., & Radford, S. E. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.08.081 · Cited by 147 · see citing works
Proteome-wide observation of the phenomenon of life on the edge of solubility
Vecchi, G., Sormanni, P., Mannini, B., Vandelli, A., Tartaglia, G. G., Dobson, C. M., Hartl, F. U., & Vendruscolo, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1910444117 · Cited by 143 · see citing works
Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins
Jeffery, C. J. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.10.001 · Cited by 142 · see citing works
Evidence for Novel β-Sheet Structures in Iowa Mutant β-Amyloid Fibrils
Tycko, R., Sciarretta, K. L., Orgel, J. P. R. O., & Meredith, S. C. (2009) · Biochemistry · doi:10.1021/bi9002666 · Cited by 140 · see citing works
Chiti, F., Lorenzi, E. D., Grossi, S., Mangione, P. P., Giorgetti, S., Caccialanza, G., Dobson, C. M., Merlini, G., Ramponi, G., & Bellotti, V. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m107040200 · Cited by 140 · see citing works
Unlike Twins: An NMR Comparison of Two α-Synuclein Polymorphs Featuring Different Toxicity
Gath, J., Bousset, L., Habenstein, B., Melki, R., Böckmann, A., & Meier, B. H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090659 · Cited by 139 · see citing works
Amyloid Fibril Polymorphism Is under Kinetic Control
Pellarin, R., Schüetz, P., Guarnera, E., & Caflisch, A. (2010) · Journal of the American Chemical Society · doi:10.1021/ja106044u · Cited by 135 · see citing works
Structure–activity relationship of amyloid fibrils
Maji, S., Wang, L., Greenwald, J., & Riek, R. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.07.003 · Cited by 130 · see citing works
Sigalov, A. B., Zhuravleva, A. V., & Orekhov, V. Y. (2007) · Biochimie · doi:10.1016/j.biochi.2006.11.003 · Cited by 128 · see citing works
Evidence for Age-Dependent in Vivo Conformational Rearrangement within Aβ Amyloid Deposits
Nyström, S., Psonka-Antonczyk, K. M., Ellingsen, P. G., Johansson, L. B. G., Reitan, N. K., Handrick, S., Prokop, S., Heppner, F. L., Wegenast‐Braun, B. M., Jucker, M., et al. (2013) · ACS Chemical Biology · doi:10.1021/cb4000376 · Cited by 111 · see citing works
Ovchinnikov, S., Kim, D. E., Wang, R. Y., Liu, Y., DiMaio, F., & Baker, D. A. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24974 · Cited by 111 · see citing works
Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation
Tian, P., Boomsma, W., Wang, Y., Otzen, D. E., Jensen, M. H., & Lindorff‐Larsen, K. (2014) · Journal of the American Chemical Society · doi:10.1021/ja5093634 · Cited by 105 · see citing works
Chameleon sequences in the PDB
Mezei, M. (1998) · Protein Engineering Design and Selection · doi:10.1093/protein/11.6.411 · Cited by 95 · see citing works
Li, Y., Zhang, C., Bell, E. W., Yu, D., & Zhang, Y. (2019) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25798 · Cited by 94 · see citing works
Zhang, C., Mortuza, S. M., He, B., Wang, Y., & Zhang, Y. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25414 · Cited by 93 · see citing works
Cellular Strategies for Regulating Functional and Nonfunctional Protein Aggregation
Gsponer, J. A., & Babu, M. M. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.09.036 · Cited by 91 · see citing works
The triple power of D³: Protein intrinsic disorder in degenerative diseases
Uversky, V. N. (2014) · Frontiers in bioscience · doi:10.2741/4204 · Cited by 90 · see citing works
Functional interactions as a survival strategy against abnormal aggregation
Masino, L., Nicastro, G., Calder, L. J., et al. (2010) · The FASEB Journal · doi:10.1096/fj.10-161208 · Cited by 80 · see citing works
Aggregation of the Acylphosphatase from Sulfolobus solfataricus
Plakoutsi, G., Taddei, N., Stefani, M., & Chiti, F. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m312961200 · Cited by 75 · see citing works
Ecology and Biogenesis of Functional Amyloids in Pseudomonas
Rouse, S. L., Matthews, S., & Dueholm, M. S. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.05.004 · Cited by 74 · 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
On the Binding of Congo Red to Amyloid Fibrils
Espargaró, A., Llabrés, S., Saupe, S. J., Curutchet, C., Luque, F. J., & Sabaté, R. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.201916630 · Cited by 73 · see citing works
Structural hot spots for the solubility of globular proteins
Ganesan, A., Siekierska, A., Beerten, J., Brams, M., Durme, J. V., Baets, G. D., van der Kant, R., Gallardo, R. U., Ramakers, M., Langenberg, T., et al. (2016) · Nature Communications · doi:10.1038/ncomms10816 · Cited by 71 · see citing works
Santos, J., Pujols, J., Pallarès, I., Iglesias, V., & Ventura, S. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.05.026 · Cited by 71 · see citing works
Self-citationSolubis: a webserver to reduce protein aggregation through mutation
Durme, J. V., Baets, G. D., van der Kant, R., Ramakers, M., Ganesan, A., Wilkinson, H. R., Gallardo, R. U., Rousseau, F., & Schymkowitz, J. W. H. (2016) · Protein Engineering Design and Selection · doi:10.1093/protein/gzw019 · Cited by 68 · see citing works
Structural and molecular basis of cross-seeding barriers in amyloids
Daskalov, A., Martinez, D., Coustou, V., Mammeri, N. E., Berbon, M., Andreas, L. B., Bardiaux, B., Stanek, J., Noubhani, A., Kauffmann, B., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2014085118 · Cited by 67 · 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
Tartaglia, G. G., & Vendruscolo, M. (2009) · Molecular BioSystems · doi:10.1039/b913099n · Cited by 61 · see citing works
Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue
Liu, J., Costantino, I. M., Venugopalan, N., Fischetti, R. F., Hyman, B. T., Frosch, M. P., Gómez‐Isla, T., & Makowski, L. (2016) · Scientific Reports · doi:10.1038/srep33079 · Cited by 59 · see citing works
Bacterial functional amyloids: Order from disorder
Jain, N., & Chapman, M. R. (2019) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2019.05.010 · Cited by 56 · see citing works
Schermeyer, M., Wöll, A. K., Kokke, B. P. A., Eppink, M. H. M., & Hubbuch, J. J. (2017) · mAbs · doi:10.1080/19420862.2017.1338222 · Cited by 55 · see citing works
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility
Gil-García, M., Bañó‐Polo, M., Varejão, N., Jamroz, M., Kuriata, A., Díaz-Caballero, M., Lascorz, J., Morel, B., Navarro, S., Reverter, D., et al. (2018) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.8b00341 · Cited by 55 · see citing works
Self-citationBaets, G. D., Reumers, J., Delgado, J., Dopazo, J., Schymkowitz, J. W. H., & Rousseau, F. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002090 · Cited by 54 · see citing works
Distinct Mechanisms Determine α-Synuclein Fibril Morphology during Growth and Maturation
Sidhu, A., Segers‐Nolten, I. M. J., Raussens, V., Claessens, M. M. A. E., & Subramaniam, V. (2016) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.6b00287 · Cited by 54 · see citing works
Wasmer, C., Zimmer, A., Sabaté, R., Soragni, A., Saupe, S. J., Ritter, C., & Meier, B. H. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.06.053 · Cited by 53 · see citing works
Minimalist Prion-Inspired Polar Self-Assembling Peptides
Díaz-Caballero, M., Navarro, S., Fuentes, I., Teixidor, F., & Ventura, S. (2018) · ACS Nano · doi:10.1021/acsnano.8b00417 · Cited by 49 · see citing works
Self-citationFunctional amyloids of eukaryotes: criteria, classification, and biological significance
Sergeeva, A. V., & Galkin, A. P. (2020) · Current Genetics · doi:10.1007/s00294-020-01079-7 · Cited by 45 · see citing works
Haarmann, C., GREEN, D. J., Casarotto, M. G., Laver, D. R., & Dulhunty, A. F. (2003) · Biochemical Journal · doi:10.1042/bj20021763 · Cited by 44 · see citing works
Cryo-EM structure of alpha-synuclein fibrilsPreprint
Guerrero-Ferreira, R., Taylor, N. M. I., Mona, D., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/276436 · Cited by 40 · see citing works
Structure of an infectious mammalian prionPreprint
Kraus, A., Hoyt, F. H., Schwartz, C. L., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.14.431014 · Cited by 40 · see citing works
Mutual Induced Fit Binding of Xenopus Ribosomal Protein L5 to 5S rRNA
DiNitto, J. P., & Huber, P. W. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00685-5 · Cited by 39 · see citing works
Theme and variations: evolutionary diversification of the HET-s functional amyloid motif
Daskalov, A., Dyrka, W., & Saupe, S. J. (2015) · Scientific Reports · doi:10.1038/srep12494 · Cited by 37 · see citing works
Discordant and chameleon sequences: Their distribution and implications for amyloidogenicity
Gendoo, D. M. A., & Harrison, P. M. (2011) · Protein Science · doi:10.1002/pro.590 · Cited by 34 · see citing works
Native Structure Protects SUMO Proteins from Aggregation into Amyloid Fibrils
Sabaté, R., Espargaró, A., Graña‐Montes, R., et al. (2012) · Biomacromolecules · doi:10.1021/bm3004385 · Cited by 34 · see citing works
Advances in the Prediction of Protein Aggregation Propensity
Pallarès, I., & Ventura, S. (2019) · Current Medicinal Chemistry · doi:10.2174/0929867324666170705121754 · Cited by 32 · see citing works
Self-citationAssociation Between Foldability and Aggregation Propensity in Small Disulfide-Rich Proteins
Fraga, H., Montes, R. G., Illa, R., Covaleda, G., & Ventura, S. (2014) · Antioxidants and Redox Signaling · doi:10.1089/ars.2013.5543 · Cited by 27 · see citing works
Self-citationSolution structure of human β-endorphin in helicogenic solvents: an NMR study
Saviano, G., Crescenzi, O., Picone, D., Temussi, P., & Tancredi, T. (1999) · Journal of Peptide Science · doi:10.1002/(sici)1099-1387(199909)5:9 · Cited by 22 · see citing works
Dual Antibody-Conjugated Amyloid Nanorods to Promote Selective Cell–Cell Interactions
Wang, W., Gil-García, M., & Ventura, S. (2021) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.0c21996 · Cited by 15 · see citing works
Self-citationComputational prediction and redesign of aberrant protein oligomerization
Santos, J., Iglesias, V., & Ventura, S. (2019) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2019.11.002 · Cited by 13 · see citing works
Self-citationChameleon sequences in neurodegenerative diseases
Bahramali, G., Goliaei, B., Minuchehr, Z., et al. (2016) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2016.01.187 · Cited by 11 · see citing works
Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation
Čarija, A., Pinheiro, F., Iglesias, V., & Ventura, S. (2019) · Cells · doi:10.3390/cells8080856 · Cited by 11 · see citing works
Self-citationBahramali, G., Goliaei, B., Minuchehr, Z., & Marashi, S. (2016) · Amino Acids · doi:10.1007/s00726-016-2361-6 · Cited by 3 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins
Agarwal, V., & McShan, A. C. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01638-w · Cited by 155 · see citing works
“However, care must be taken when interpreting predictions, as highlighted by the incorrect AF2 model of the β-endorphin amyloid fiber relative to its experimental solid-state NMR structure 58 (Fig.”
MethodAlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function
Laurents, D. V. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.906437 · Cited by 95 · see citing works
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 · see citing works
The Epigenetic Dimension of Protein Structure Is an Intrinsic Weakness of the AlphaFold Program
Azzaz, F., Yahi, N., Chahinian, H., & Fantini, J. (2022) · Biomolecules · doi:10.3390/biom12101527 · Cited by 53 · see citing works
- Authors
- Pinheiro, F., Santos, J., & Ventura, S.
- Affiliations
- Universitat Autònoma de Barcelona (ES)
- Corresponding author
- Pinheiro, Francisca
- Ventura, Salvador
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2021-10
- Volume
- 433
- Issue
- 20
- Pages
- 167059
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W3165398695
- Cited by
- 88
- References
- 164
- Citations by year
- 2026: 7 · 2025: 13 · 2024: 16 · 2023: 30 · 2022: 15 · 2021: 7
- FWCI
- 1.78
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Universitat Autònoma de Barcelona (FPU17/01157)
- Institució Catalana de Recerca i Estudis Avançats
- Ministerio de Ciencia e Innovación (PID2019-105017RB-I00)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Prion Diseases and Protein Misfolding
- Keywords
- AlphaFold, protein aggregation, amyloid polymorphism, functional amyloids, amyloidosis, aggregation intermediates, protein structure prediction, structure-activity relationship
- MeSH terms
- Amyloid, Amyloidosis, Animals, Humans, Models, Molecular, Protein Conformation, Software, Protein Folding, Protein Aggregation, Pathological, Protein Aggregates
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