ArticleJournal of chemical information and modeling2021
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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Who cites it
129 citing papers in PubMed.
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- Genomic and Molecular Interaction Analysis of NodD1 in a Novel Bradyrhizobium yuanmingense sp. B64 Isolate for Nodulation and Symbiosis of Legume Plants.Biochemical genetics · 2026Article
- The influence of ligands on AlphaFold3 prediction of cryptic pockets.Communications biology · 2026Article
- Evaluation of ADP Glucose Pyrophosphorylase Subunit Interaction in Wheat by Binding Free Energy Calculations.Molecular biotechnology · 2026Article
- Designing of a conserved subunit multiepitope vaccine candidate against Francisella tularensis Schu S4 using immunoinformatics.Scientific reports · 2026Article
- Structural choreography of bacteriophage N4 ejection proteins and the giant virion-associated RNA polymerase.Nature communications · 2026Article
- AlphaInterp: Mechanistic Interpretability of AlphaFold 3 Reveals How Evolutionary Information Shapes Protein Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- A platform to design and optimise fluorogenic scFvs for detection of interleukin 33.Chemical science · 2026Article
- Multimodal computational discovery of MvfR inhibitors targeting quorum sensing in multi-drug-resistant Pseudomonas aeruginosa.Scientific reports · 2026Article
- From Sequence to Solution: Computational Design of a Multi-Epitope Vaccine Candidate Against Francisella tularensis.Probiotics and antimicrobial proteins · 2026Article
- Comparative study of two xanthan gum glycosyltransferases combining AI structure predictions and molecular modeling.bioRxiv : the preprint server for biology · 2026Article
- A New Model for the Transmembrane Heterocomplex of Hemagglutinin HA and Ionic Channel M2 Proteins in Influenza A Virus.Doklady. Biochemistry and biophysics · 2026Article
- Controlled Optically Active Hierarchical Nanostructures of Side-Chain Sequence-Regulated Graphene Nanoribbons.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Bias in the AlphaFold3 prediction of ligand-induced domain motion in enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The transformative impact of AI-enabled AlphaFold 3: evolution, current status, and future prospects in structural biology.Frontiers in artificial intelligence · 2026Review
- An integrative coding and non-coding SNPs analysis of theFrontiers in oncology · 2026Article
- Protein structure prediction powered by artificial intelligence: from biochemical foundations to practical applications.Frontiers in molecular biosciences · 2026Review
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 2026Article
- Designing modular genetic sensors with TtgR/AcrR family transcriptional regulators by using a statistical and data-driven approach.Nucleic acids research · 2025Article
69 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
AlphaFold 2 (AF2) was the star of CASP14, the last biannual structure prediction experiment. Using novel deep learning, AF2 predicted the structures of many difficult protein targets at or near experimental resolution. Here, we present our perspective of why AF2 works and show that it is a very sophisticated fold recognition algorithm that exploits the completeness of the library of single domain PDB structures. It has also learned local side chain packing rearrangements that enable it to refine proteins to high resolution. The benefits and limitations of its ability to predict the structures of many more proteins at or close to atomic detail are discussed.
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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.