Predicting Protein Interaction Sites Through Machine Learning and Data Aggregation

Abstract

As biological processes are carried out predominantly by proteins, the accurate annotation of protein function is key to understanding life at the molecular level. Modern sequencing technologies can identify a vast number of proteins quickly and accurately at a pace that far exceeds our ability to annotate them experimentally. Thus, computational approaches play a key role in protein annotation. Fundamental aspects of a protein’s functionality can be uncovered by its interactions as proteins accomplish nearly all their activities via binding to various ligands. The interactions of proteins with other molecules are mediated by specific amino acids, and their identification is crucial for understanding how a specific protein performs its role. Therefore, identifying which protein residues mediate which interaction can help in narrowing the functional annotation gap.In this dissertation, I introduce novel computational approaches that leverage different data aggregation levels and different prior knowledge to predict interaction sites in proteins. First, I explore which properties of proteins are predictive of interaction sites. I analyze and encode numerous site-based properties that can be derived from sequence alone. My approach leverages protein domains–fundamental units within proteins that correspond to families that share sequence, structure, and evolutionary descent–and I introduce features extracted from them. Next, I rely on these predictive features and introduce a framework of supervised machine learning algorithms to predict interaction sites within protein domains. Finally, I utilize complete protein sequences and extend beyond standard supervised machine learning algorithms to develop predictors based on deep neural networks pretrained on unlabelled protein sequences. Together, these approaches provide a framework for predicting protein interaction sites to expand our knowledge of protein molecular interactions.