Bioinformatics Commons^™

Deep Learning Methods For Prediction Of And Escape From Protein Recognition, Bowen Dai

Dartmouth College Ph.D Dissertations

Protein interactions drive diverse processes essential to living organisms, and thus numerous biomedical applications center on understanding, predicting, and designing how proteins recognize their partners. While unfortunately the number of interactions of interest still vastly exceeds the capabilities of experimental determination methods, computational methods promise to fill the gap. My thesis pursues the development and application of computational methods for several protein interaction prediction and design tasks. First, to improve protein-glycan interaction specificity prediction, I developed GlyBERT, which learns biologically relevant glycan representations encapsulating the components most important for glycan recognition within their structures. GlyBERT encodes glycans with a branched …