ArticleProceedings of the National Academy of Sciences of the United States of America2024
AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed.
- Embrace Disorder as a Function: Bio-Informed Biomaterials Design Advanced by Intrinsically Disordered Proteins.Biomimetics (Basel, Switzerland) · 2026Article
- Integrating Epistatic Interactions into Genomic Prediction of Growth and Fillet Fat Content in Common Carp.International journal of molecular sciences · 2026Article
- CDK12/13 inhibition overcomes platinum resistance by impairing RNA metabolism.Signal transduction and targeted therapy · 2026Article
- NADPH oxidases in immunometabolism and disease pathology: mechanistic networks, pollutant triggers, and therapeutic frontiers.Cellular & molecular immunology · 2026Review
- Autosomal recessive MALTA syndrome with compound heterozygousJID innovations : skin science from molecules to population health · 2026Article
- Discovering host-viral protein interactions in autophagy: A LIR discovery pipeline for identifying LC3-interacting region motifs in highly virulent viruses.PLoS pathogens · 2026Article
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- Protein-protein interaction-mediated signaling networks in ischemic stroke: from molecular mechanisms to therapeutic strategies.Acta pharmacologica Sinica · 2026Review
- When can AlphaFold predict the oligomeric states of proteins?Protein science : a publication of the Protein Society · 2026Article
- Molecular interplay between sperm and oocyte: a narrative review.Human reproduction update · 2026Review
- Symbiotic peptides modulate rhizobial physiology without terminal differentiation.Science advances · 2026Article
- Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families.BioData mining · 2026Review
- Evidence for the Formation of Metabolons Surrounding the Pyruvate Node in the Supercritical COACS omega · 2026Article
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- Insulin receptor trafficking and interactions in muscle cells.Journal of the Endocrine Society · 2026Article
- A Comparative Review of Artificial Intelligence Applications in Small Molecule Versus Peptide Drug Discovery.International journal of molecular sciences · 2026Review
- Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex.bioRxiv : the preprint server for biology · 2026Article
- AI-Assisted Computed Structure Models for Pre-Ubiquitylation Complexes Assembled by Respiratory Syncytial Viral Suppressors of Cellular Interferon Response.International journal of molecular sciences · 2026Article
- A Survey of Predicted Protein-Protein Interactions Involving Disordered Regions in Humans.Journal of molecular biology · 2026Article
- Dense and distributed neuropeptide network in the nerve net of Hydra vulgaris.PLoS computational biology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Interactions mediated by intrinsically disordered protein regions (IDRs) pose formidable challenges in structural characterization. IDRs are highly versatile, capable of adopting diverse structures and engagement modes. Motivated by recent strides in protein structure prediction, we embarked on exploring the extent to which AlphaFold-Multimer can faithfully reproduce the intricacies of interactions involving IDRs. To this end, we gathered multiple datasets covering the versatile spectrum of IDR binding modes and used them to probe AlphaFold-Multimer's prediction of IDR interactions and their dynamics. Our analyses revealed that AlphaFold-Multimer is not only capable of predicting various types of bound IDR structures with high success rate, but that distinguishing true interactions from decoys, and unreliable predictions from accurate ones is achievable by appropriate use of AlphaFold-Multimer's intrinsic scores. We found that the quality of predictions drops for more heterogeneous, fuzzy interaction types, most likely due to lower interface hydrophobicity and higher coil content. Notably though, certain AlphaFold-Multimer scores, such as the Predicted Aligned Error and residue-ipTM, are highly correlated with structural heterogeneity of the bound IDR, enabling clear distinctions between predictions of fuzzy and more homogeneous binding modes. Finally, our benchmarking revealed that predictions of IDR interactions can also be successful when using full-length proteins, but not as accurate as with cognate IDRs. To facilitate identification of the cognate IDR of a given partner, we established "minD," which pinpoints potential interaction sites in a full-length protein. Our study demonstrates that AlphaFold-Multimer can correctly identify interacting IDRs and predict their mode of engagement with a given partner.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.