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References from AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins. Local targets link to admitted publications; unresolved targets remain external evidence.
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Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction. arXiv
2024 · External reference
Unresolved reference
2024 · External reference
10.1016/j.bbrc.2006.01.159
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RepeatsDB: a database of tandem repeat protein structures
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VERIFY3D: assessment of protein models with three-dimensional profiles
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AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder
10.1093/nar/gkae385 · 2024 · External reference
Anchored clathrate waters bind antifreeze proteins to ice
2011 · External reference
10.1002/1097-0134(20001101)41:2<224::aid-prot70>3.0.co;2-z
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More than just pattern recognition: prediction of uncommon protein structure features by AI methods
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10.1063/1.445869 · External reference
Highly accurate protein structure with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
10.1016/j.jsb.2011.08.009
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β-rolls, β-helices, and other β-solenoid proteins
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10.1073/pnas.012608599
10.1073/pnas.012608599 · External reference
Generalized biomolecular modeling and design with RoseTTAFold all-atom
10.1126/science.adl2528 · 2024 · External reference
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10.1126/science.2503871 · External reference
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10.1126/science.ade2574 · External reference
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10.1101/2024.03.07.583852 · External reference
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10.1038/nbt.2419 · External reference
Introduction to protein crystallization
10.1107/s2053230x13033141 · 2014 · External reference
Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space
10.1016/j.jsb.2023.108010 · 2023 · External reference
10.1002/jcc.21787
10.1002/jcc.21787 · External reference
ColabFold: making protein folding accessible to all
10.1038/s41592-022-01488-1 · 2022 · External reference
10.1093/oxfordjournals.molbev.a026406
10.1093/oxfordjournals.molbev.a026406 · External reference
10.1093/nar/gkaa913
10.1093/nar/gkaa913 · External reference
Unresolved reference
External reference
Folding the unfoldable: using AlphaFold to explore spurious proteins
10.1093/bioadv/vbab043 · 2022 · External reference
10.1101/2024.07.10.602726
10.1101/2024.07.10.602726 · External reference
10.1126/science.1158868
10.1126/science.1158868 · External reference
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10.1093/bioinformatics/btt055 · External reference
10.1073/pnas.95.23.13363
10.1073/pnas.95.23.13363 · External reference
State-of-the-art estimation of protein model accuracy using AlphaFold
10.1103/physrevlett.129.238101 · 2022 · External reference
10.1007/978-981-32-9449-3_14
10.1007/978-981-32-9449-3_14 · External reference
10.1002/prot.26593
10.1002/prot.26593 · External reference
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10.1101/2024.09.08.611582 · External reference
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10.1093/bioinformatics/btu739 · External reference
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10.1145/3580305.3599337 · External reference
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10.1002/jcc.20291 · External reference
10.1038/s41587-023-01773-0
10.1038/s41587-023-01773-0 · External reference
10.1093/nar/gkad1011
10.1093/nar/gkad1011 · External reference
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10.1101/2024.07.09.602655 · External reference
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10.21105/joss.04200 · External reference
10.1093/bioinformatics/btq066
10.1093/bioinformatics/btq066 · External reference
10.1002/prot.20264
10.1002/prot.20264 · External reference
10.1016/j.jmb.2017.12.007
10.1016/j.jmb.2017.12.007 · External reference
