ArticleFrontiers in molecular biosciences2022
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.
Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 51 citations in OpenAlex.
- Review
- The influence of ligands on AlphaFold3 prediction of cryptic pockets.Communications biology · 2026Article
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
- Unlocking the secrets of SARS-CoV-2 nsp3 by combining experiments with AlphaFold2 domain prediction.Life science alliance · 2026Article
- Modernizing biomolecular NMR: The POKY suite.The Journal of biological chemistry · 2026Review
- Structure of the disulfide-rich modules of a striking tandem repeat protein, avian cysteine-rich eggshell membrane protein.Protein science : a publication of the Protein Society · 2026Article
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.Proteins · 2026Article
- In silico pharmacological analysis of Tinospora cordifolia compounds targeting African swine fever virus B175L.PloS one · 2026Article
- Assisting and accelerating NMR assignment with restrained structure prediction.Communications biology · 2025Article
- Leveraging AlphaFold2 and residual dipolar couplings for side-chain methyl group assignment: A case study with S. cerevisiae Xrs2.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2025Article
- Small Disulfide Proteins with Antifungal Impact: NMR Experimental Structures as Compared to Models of Alphafold Versions.International journal of molecular sciences · 2025Article
- Artificial intelligence in drug development: reshaping the therapeutic landscape.Therapeutic advances in drug safety · 2025Review
- Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Insights into AlphaFold's breakthrough in neurodegenerative diseases.Irish journal of medical science · 2024Review
- Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data.bioRxiv : the preprint server for biology · 2024Article
- The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins.Nature chemical biology · 2024Review
- AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!Journal of magnetic resonance (San Diego, Calif. : 1997) · 2024Article
- A predicted model-aided reconstruction algorithm for X-ray free-electron laser single-particle imaging.IUCrJ · 2024Article
- The origin and structural evolution of de novo genes in Drosophila.Nature communications · 2024Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR and cryo-electron microscopy structures. Here we assess the hypothesis that AlphaFold models of small, relatively rigid proteins have accuracies (based on comparison against experimental data) similar to experimental solution NMR structures. We selected six representative small proteins with structures determined by both NMR and X-ray crystallography, and modeled each of them using AlphaFold. Using several structure validation tools integrated under the Protein Structure Validation Software suite (PSVS), we then assessed how well these models fit to experimental NMR data, including NOESY peak lists (RPF-DP scores), comparisons between predicted rigidity and chemical shift data (ANSURR scores), and
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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.