ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification
英文:
ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification
<jats:title>Abstract</jats:title>
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<jats:title>Motivation</jats:title>
<jats:p>Protein–protein interactions are essential for the cell and mediate various functions. However, mutations can disrupt these interactions and may cause diseases. Currently available computational methods require a complex structure as input for predicting the change in binding affinity. Further, they have not included the functional class information for the protein–protein complex. To address this, we have developed a method, ProAffiMuSeq, which predicts the change in binding free energy using sequence-based features and functional class.</jats:p>
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<jats:title>Results</jats:title>
<jats:p>Our method shows an average correlation between predicted and experimentally determined ΔΔG of 0.73 and mean absolute error (MAE) of 0.86 kcal/mol in 10-fold cross-validation and correlation of 0.75 with MAE of 0.94 kcal/mol in the test dataset. ProAffiMuSeq was also tested on an external validation set and showed results comparable to structure-based methods. Our method can be used for large-scale analysis of disease-causing mutations in protein–protein complexes without structural information.</jats:p>
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<jats:title>Availability and implementation</jats:title>
<jats:p>Users can access the method at https://web.iitm.ac.in/bioinfo2/proaffimuseq/.</jats:p>
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<jats:title>Supplementary information</jats:title>
<jats:p>Supplementary data are available at Bioinformatics online.</jats:p>
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