FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework

Nonsynonymous single-nucleotide polymorphisms (nsSNPs), implicated in over 6000 diseases, necessitate accurate prediction for expedited drug discovery and improved disease diagnosis. In this study, we propose FCMSTrans, a novel nsSNP predictor that innovatively combines the transformer framework and multiscale modules for comprehensive feature extraction. The distinctive attribute of FCMSTrans resides in a deep feature combination strategy. This strategy amalgamates evolutionary-scale modeling (ESM) and ProtTrans (PT) features, providing an understanding of protein biochemical properties, and position-specific scoring matrix, secondary structure, predicted relative solvent accessibility, and predicted disorder (PSPP) features, which are derived from four protein sequences and structure-oriented characteristics. This feature combination offers a comprehensive view of the molecular dynamics involving nsSNPs. Our model employs the transformer's self-attention mechanisms across multiple layers, extracting higher-level and abstract representations. Simultaneously, varied-level features are captured by multiscale convolutions, enriching feature abstraction at multiple echelons. Our comparative analyses with existing methodologies highlight significant improvements made possible by the integrated feature fusion approach adopted in FCMSTrans. This is further substantiated by performance assessments based on diverse data sets, such as PredictSNP, MMP, and PMD, with areas under the curve (AUCs) of 0.869, 0.819, and 0.693, respectively. Furthermore, FCMSTrans shows robustness and superiority by outperforming the current best predictor, PROVEAN, in a blind test conducted on a third-party data set, achieving an impressive AUC score of 0.7838. The Python code of FCMSTrans is available at https://github.com/gc212/FCMSTrans for academic usage.