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AlphaFold 2.0 was used to assess the AntiFam database of spurious protein sequences. While most showed no structure, one entry was predicted as globular, validating AlphaFold as a quality control. Short sequences require careful interpretation.

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Area of Science:

  • * Computational biology
  • * Structural bioinformatics
  • * Protein sequence analysis

Background:

  • * AlphaFold 2.0 significantly advanced protein structure prediction from amino acid sequences.
  • * The AntiFam database contains protein sequence families suspected to be spurious translations.
  • * The structural integrity of AntiFam sequences is largely uncharacterized.

Purpose of the Study:

  • * To computationally determine the structures of representative sequences from the AntiFam database using AlphaFold 2.0.
  • * To evaluate the AntiFam resource using AlphaFold 2.0 predictions.
  • * To assess AlphaFold 2.0's performance on potentially non-globular protein sequences.

Main Methods:

  • * Employed AlphaFold 2.0 for structure prediction of representative sequences from all AntiFam 6.0 families.
  • * Analyzed prediction confidence scores (pLDDT) to assess structural integrity.
  • * Investigated trends between sequence length and prediction confidence.

Main Results:

  • * The vast majority of AntiFam sequences did not yield predictions of well-ordered globular structures.
  • * One AntiFam entry was predicted to form a globular structure, suggesting it may represent a bona fide protein.
  • * A trend was observed where shorter sequences (<100 amino acids) exhibited higher mean pLDDT scores.
  • * Six out of 131 short AntiFam sequences received a mean pLDDT ≥ 80.

Conclusions:

  • * AlphaFold 2.0 can serve as a valuable quality control tool for protein sequence databases like AntiFam.
  • * The AntiFam database provides a useful set of known spurious proteins for quality control of AlphaFold predictions.
  • * Caution is advised when interpreting AlphaFold 2.0 predictions for short protein sequences due to potential biases in confidence scores.