Alexander Derry

Research

Self-supervised representation learning on protein structure

Deep learning for protein structure analysis

Protein function prediction and annotation

Benchmarking and dataset curation

Drug discovery and repurposing

Derry, A., & Altman, R. (2022). COLLAPSE: A representation learning framework for identification and characterization of protein structural sites. Protein Science, 32(2), e4541. https://doi.org/10.1002/pro.4541
Townshend, R., Vögele, M., Suriana, P., Derry, A., Powers, A., Laloudakis, Y., Balachandar, S., Jing, B., Anderson, B., Eismann, S., Kondor, R., Altman, R., & Dror, R. (2021). ATOM3D: Tasks On Molecules in Three Dimensions. NeurIPS 2021 Datasets and Benchmarks Track. https://arxiv.org/abs/2012.04035
Derry, A., Carpenter, K., & Altman, R. (2021). Training data composition affects performance of structure analysis algorithms.. Pacific Symposium on Biocomputing 2022, 10-22. https://doi.org/10.1101/2021.09.30.462647v2
Sosa, D., Derry, A., Guo, M., Wei, E., Brinton, C., & Altman, R. (2019). A literature-based knowledge graph embedding method for identifying drug repurposing opportunities in rare diseases. Pacific Symposium on Biocomputing 2020, 463-474. https://doi.org/10.1142/9789811215636_0041