3260 papers • 126 benchmarks • 313 datasets
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly sought after as they could yield significant advances in drug discovery and design as well as protein function analysis.
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This work considers the prediction of interfaces between proteins, a challenging problem with important applications in drug discovery and design, and examines the performance of existing and newly proposed spatial graph convolution operators for this task.
The first end-to-end learning model for protein interface prediction, the Siamese Atomic Surfacelet Network (SASNet), is developed and it is found that SASNet outperforms state-of-the-art methods trained on gold-standard structural data, even when trained on only 3% of the new dataset.
It is demonstrated through rigorous benchmarks that training an existing state-of-the-art (SOTA) model for PIP on DIPS-Plus yields new SOTA results, surpassing the performance of some of the latest models trained on residue-level and atom-level encodings of protein complexes to date.
Strong evidence indicates that the incorporation of protein language models’ knowledge enhances geometric networks’ capacity by a significant margin and can be generalized to complex tasks.
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