ReviewJournal of the Royal Society, Interface2025
Emerging frontiers in protein structure prediction following the AlphaFold revolution.
Review in Journal of the Royal Society, Interface, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- HighFold4: extending AlphaFold3 to accurate cyclic peptide conformation prediction via custom chemical connectivity.Briefings in bioinformatics · 2026Article
- Biosynthesis and Microbial Production of Carminic Acid: From Pathway Elucidation to Synthetic Biology.Microorganisms · 2026Review
- Modular integration of nanopore sequencing, alphafold modeling, and statistical design boosts 1-hydroxyphenazine yield in Pseudomonas aeruginosa strain KAEH25.BMC microbiology · 2026Article
- Continuous negative autoregulation fine-tunes dosage-sensitive transcription factor expression to maintain post-mitotic neuron identity.bioRxiv : the preprint server for biology · 2026Article
- Biophysical and enzymatic comparison ofbioRxiv : the preprint server for biology · 2026Article
- Modulation of Fructose Transfer Process for Promoting Apparent Isomerization Activity of Amylosucrase fromJournal of agricultural and food chemistry · 2026Article
- The transformative impact of AI-enabled AlphaFold 3: evolution, current status, and future prospects in structural biology.Frontiers in artificial intelligence · 2026Review
- Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching.bioRxiv : the preprint server for biology · 2025Article
- Cell type-specific functions of the PBAF chromatin-remodeling complex in neuronal diversification.Nature communications · 2025Article
- TruMPET: A New Method for Protein Secondary Structure Prediction Using Neural Networks Trained on Multiple Pre-Selected Physicochemical and Structural Features.International journal of molecular sciences · 2025Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Models of protein structures enable molecular understanding of biological processes. Current protein structure prediction tools lie at the interface of biology, chemistry and computer science. Millions of protein structure models have been generated in a very short space of time through a revolution in protein structure prediction driven by deep learning, led by AlphaFold. This has provided a wealth of new structural information. Interpreting these predictions is critical to determining where and when this information is useful. But proteins are not static nor do they act alone, and structures of proteins interacting with other proteins and other biomolecules are critical to a complete understanding of their biological function at the molecular level. This review focuses on the application of state-of-the-art protein structure prediction to these advanced applications. We also suggest a set of guidelines for reporting AlphaFold predictions.
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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.