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Workshop: Machine Learning in Structural Biology Workshop

Structure, Surface and Interface Informed Protein Language Model

Ioan Ieremie


Language models applied to protein sequence data have gained a lot of interest in recent years, mainly due to their ability to capture complex patterns at the protein sequence level. However, their understanding of why certain evolution-related conservation patterns appear is limited. This work explores the potential of protein language models to further incorporate intrinsic protein properties stemming from protein structures, surfaces, and interfaces. The results indicate that this multi-task pretraining allows the PLM to learn more meaningful representations by leveraging information obtained from different protein views. We evaluate and show improvements in performance on various downstream tasks, such as enzyme classification, remote homology detection, and protein engineering datasets.

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