ArticleJournal of chemical information and modeling2025
Structure Prediction of Alternate Frame Folding Systems with AlphaFold3.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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Who cites it
4 citing papers in PubMed.
- Biasing Conformational Sampling in AlphaFold 3 and Boltz-2 via Pair Representation Scaling.Journal of chemical information and modeling · 2026Article
- Deep learning-based structural prediction (AlphaFold 3) of shrimp IMNV RdRp and identification of seaweed-derived metabolites for antiviral intervention in aquaculture.Virus research · 2026Article
- Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways.Journal of chemical theory and computation · 2026Article
- Structural quality-tier assessment for TCR-pMHC functional enrichment.Frontiers in immunology · 2026Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
AlphaFold has proven to be a valuable tool for predicting protein structures with unprecedented speed and accuracy. Extensive research from multiple groups has demonstrated that manipulating the multiple sequence alignment used for structure prediction can enhance AlphaFold2's ability to explore protein conformational landscapes, yielding reliable models of proteins capable of switching between alternative conformations. The release of the thoroughly reengineered AlphaFold3, which promises even greater prediction accuracy and efficiency, raises the question of whether such alternative conformational states can be modeled-either natively or by tuning the multiple sequence alignment used for prediction. In this work, we use a family of green fluorescent proteins engineered through alternate frame folding to assess AlphaFold3's prediction accuracy and uncover an unexpected role of disordered regions in driving the conformational preferences of the models.
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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.