Navigating the unstructured by evaluating alphafold’s efficacy in predicting missing residues and structural disorder in proteins

Sen Zheng

PLOS ONE, 2025, vol. 20, issue 3, 1-21

Abstract: The study investigated regions with undefined structures, known as “missing” segments in X-ray crystallography and cryo-electron microscopy (Cryo-EM) data, by assessing their predicted structural confidence and disorder scores. Utilizing a comprehensive dataset from the Protein Data Bank (PDB), residues were categorized as “modeled”, “hard missing” and “soft missing” based on their visibility in structural datasets. Key features were determined, including a confidence score predicted local distance difference test (pLDDT) from AlphaFold2, an advanced structural prediction tool, and a disorder score from IUPred, a traditional disorder prediction method. To enhance prediction performance for unstructured residues, we employed a Long Short-Term Memory (LSTM) model, integrating both scores with amino acid sequences. Notable patterns such as composition, region lengths and prediction scores were observed in unstructured residues and regions identified through structural experiments over our studied period. Our findings also indicate that “hard missing” residues often align with low confidence scores, whereas “soft missing” residues exhibit dynamic behavior that can complicate predictions. The incorporation of pLDDT, IUPred scores, and sequence data into the LSTM model has improved the differentiation between structured and unstructured residues, particularly for shorter unstructured regions. This research elucidates the relationship between established computational predictions and experimental structural data, enhancing our ability to target structurally significant areas for research and guiding experimental designs toward functionally relevant regions.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0313812

DOI: 10.1371/journal.pone.0313812

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