ArticleComputational and structural biotechnology journal2025
Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment.
Article in Computational and structural biotechnology journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.Computational and structural biotechnology journal · 2026Article
- AlphaFold3: An Overview of Applications and Performance Insights.International journal of molecular sciences · 2025Review
- AlphaFold in protein structure and function prediction.Computational and structural biotechnology journal · 2025Article
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3 authors.
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Abstract
A key step in protein structure prediction involves the detection of co-evolving pairs of residues, a signal for spatial proximity. This information is gleaned from multiple sequence alignment and underscores Alphafold's structure prediction for almost every known protein. A simple means to create proteins beyond those found in nature, is by unnaturally fusing together two known proteins or protein parts. Here we demonstrate that structured peptides are predicted with significantly reduced accuracy when added to the terminal ends of scaffold proteins. Appending the multiple sequence alignment for the individual peptide tags to that of the scaffold protein often restores prediction accuracy. This work suggests that this windowed multiple sequence alignment approach can be a useful tool for predicting the structure of fused, chimeric proteins.
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