ArticleScientific reports2022
AlphaFold2 models indicate that protein sequence determines both structure and dynamics.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers.
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144 citing papers in PubMed.
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- AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level.Protein science : a publication of the Protein Society · 2026Article
- Innovative approaches to therapeutic target discovery amid the global challenge of antimicrobial resistance.Journal of computer-aided molecular design · 2026Review
- Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity.Acta crystallographica. Section F, Structural biology communications · 2026Article
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- Inhibition of the QPCT-PDIA4 axis rescues ΔF508 and N1303K CFTR in cystic fibrosis.Nature communications · 2026Article
- ROWVA: A Structure-Based Metric for Predicting the Pathogenicity of Protein Variants Using Alphafold2.Cancer science · 2026Article
- Shrew is an essential, recently evolved, Drosophila specific gene required for formation of the embryonic BMP activity gradient.Developmental biology · 2026Article
- One-site polarity switch enhances catalytic efficiency and stability of D-allulose 3-epimerase via flexibility-rigidity rebalancing.Scientific reports · 2026Article
- Structural mechanism for noncanonical GPCR signaling in the Hedgehog pathway.Nature structural & molecular biology · 2026Article
- Multiple disulfide-bonded states confer extensive conformational diversity in fibrinogen.Protein science : a publication of the Protein Society · 2026Article
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
- Beyond a Passive Tether: Structural Insights into the Disordered Tail of Hsp90.Journal of the American Chemical Society · 2026Article
- Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders.International journal of molecular sciences · 2026Review
84 more citing papers are in PubMed but not listed here.
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13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.
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