PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids

• Main Authors: Vineet Singh, Alok Sharma, Abdollah Dehzangi, Tatushiko Tsunoda
• Format: Article
• Language: English
• Published: MDPI AG 2020-11-01
• Series: Genes
• Subjects: post-translational modification (PTM); lysine pupylation; structural features; protein sequences; amino acids; prediction
• Online Access: https://www.mdpi.com/2073-4425/11/12/1431

Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimental practice to detect pupylation sites proved to be expensive and requires a lot of time and resources. Thus, there have been many computational predictors developed to challenge this issue. However, performance is still limited. In this study, we propose another computational method, named PupStruct, which uses the structural information of amino acids with a radial basis kernel function Support Vector Machine (SVM) to predict pupylated lysine residues. We compared PupStruct with three state-of-the-art predictors from the literature where PupStruct has validated a significant improvement in performance over them with statistical metrics such as sensitivity (0.9234), specificity (0.9359), accuracy (0.9296), precision (0.9349), and Mathew’s correlation coefficient (0.8616) on a benchmark dataset.