2024
DOI: 10.1101/2024.04.09.588596
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Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions

Ernst W. Schmid,
Johannes C. Walter

Abstract: Protein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying biochemical processes is lacking. Although AlphaFold-Multimer (AF-M) has the potential to fill this knowledge gap, standard AF-M confidence metrics do not reliably separate relevant PPIs from an abundance of false positive predictions. To address this limitation, we used machine learning on well curated datasets to train a Structure Prediction and Omics informed Classifier calle… Show more

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Cited by 14 publications
(3 citation statements)
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“…To address this, we have incorporated a machine learning method that enhances prediction accuracy by integrating these scores with a comprehensive set of omics and structural data. This integrated approach is encapsulated in the Structure Prediction and Omics-based Classifier (SPOC), specifically designed to evaluate the validity of predicted protein interactions more effectively [Schmid EW et al 2024]. A SPOC score of 0.3 or higher is considered indicative of a high likelihood that the predicted interaction is biologically meaningful and spurious.…”
Section: Molecular Basis Of Human A4galt Dimerizationmentioning
confidence: 99%
See 1 more Smart Citation
“…To address this, we have incorporated a machine learning method that enhances prediction accuracy by integrating these scores with a comprehensive set of omics and structural data. This integrated approach is encapsulated in the Structure Prediction and Omics-based Classifier (SPOC), specifically designed to evaluate the validity of predicted protein interactions more effectively [Schmid EW et al 2024]. A SPOC score of 0.3 or higher is considered indicative of a high likelihood that the predicted interaction is biologically meaningful and spurious.…”
Section: Molecular Basis Of Human A4galt Dimerizationmentioning
confidence: 99%
“…Structure Prediction and Omics-based Classifier (SPOC) is a machine learning tool that integrates structural predictions with omics data to assess the reliability of predicted proteinprotein interactions [Schmid EW et al 2024]. It is valuable for distinguishing true interactions from false positives, offering a robust metric that enhances confidence in computational biology studies.…”
Section: Dimer Structure Analysismentioning
confidence: 99%
“…Each of the 7,608 proteins was "folded" with an H. sapiens H2A-H2B dimer in ColabFold, and each trimeric protein combination was predicted using 3 of 5 Al-phaFold-Multimer models, yielding a total of 22,824 predicted structures (Methods). Although several analysis methods have been developed to rank predictions from large scale AlphaFold multimer screens, such as pDOCKQ2 10 and SPOC score 11 , these methods are not suitable for identifying specific types of interactions such as those that occur during acidic patch binding. We therefore created a novel analysis pipeline specifically designed to examine residue interactions required for acidic patch binding.…”
Section: In Silico Protein Interaction Screening Reveals the Predicto...mentioning
confidence: 99%