Physical Sciences and Mathematics Commons^™

Computational Methods For Predicting Protein-Protein Interactions And Binding Sites, Yiwei Li

Electronic Thesis and Dissertation Repository

Proteins are essential to organisms and participate in virtually every process within cells. Quite often, they keep the cells functioning by interacting with other proteins. This process is called protein-protein interaction (PPI). The bonding amino acid residues during the process of protein-protein interactions are called PPI binding sites. Identifying PPIs and PPI binding sites are fundamental problems in system biology.

Experimental methods for solving these two problems are slow and expensive. Therefore, great efforts are being made towards increasing the performance of computational methods.

We present DELPHI, a deep learning based program for PPI site prediction and SPRINT, an algorithmic …

Discrimination Of Leucine And Isoleucine In De Novo Peptide Sequencing Using Deep Neural Networks, Bingran Shen

Electronic Thesis and Dissertation Repository

De novo peptide sequencing from tandem MS data is a key technology in proteomics for understanding the structure of proteins, especially for first seen sequences. Although this technique has advanced rapidly in recent years and become more effective, one crucial problem remained unsolved. Due to the isomerism of leucine and isoleucine, they are practically indistinguishable in de novo sequencing using traditional tandem MS data. Some experimental attempts have been made to resolve this ambiguity such as EThCD fragmentation process. In this study, we took a data focused approach rather than only looking for characteristic satellite ions produced by the EThCD …