ArticleNature methods2023
AlphaFill: enriching AlphaFold models with ligands and cofactors.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 270 papers.
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Who cites it
270 citing papers in PubMed.
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- Discovery of a phenazine-thiol conjugase from sparse data using genome-informed machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Target identification and assessment in the era of AI.Nature reviews. Drug discovery · 2026Review
- Probe-based identification of metal-binding sites using deep learning representations.Nature communications · 2026Article
- Ancestral Protein Reconstruction Uncovers a Thermotolerant Rieske Oxygenase with EnhancedACS synthetic biology · 2026Article
- Identification ofApplied and environmental microbiology · 2026Article
210 more citing papers are in PubMed but not listed here.
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Artificial intelligence-based protein structure prediction approaches have had a transformative effect on biomolecular sciences. The predicted protein models in the AlphaFold protein structure database, however, all lack coordinates for small molecules, essential for molecular structure or function: hemoglobin lacks bound heme; zinc-finger motifs lack zinc ions essential for structural integrity and metalloproteases lack metal ions needed for catalysis. Ligands important for biological function are absent too; no ADP or ATP is bound to any of the ATPases or kinases. Here we present AlphaFill, an algorithm that uses sequence and structure similarity to 'transplant' such 'missing' small molecules and ions from experimentally determined structures to predicted protein models. The algorithm was successfully validated against experimental structures. A total of 12,029,789 transplants were performed on 995,411 AlphaFold models and are available together with associated validation metrics in the alphafill.eu databank, a resource to help scientists make new hypotheses and design targeted experiments.
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