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Showing 1–5 of 5 results
Advanced filters: Author: Sophia Vincoff Clear advanced filters

  • PTM-Mamba is a post-translational modification-aware protein language model that integrates PTM tokens with bidirectional Mamba blocks and ESM-2 embeddings, enabling modeling of both wild-type and post-translationally modified sequences for diverse downstream applications.

    • Fred Zhangzhi Peng
    • Chentong Wang
    • Pranam Chatterjee
    ResearchOpen Access
    Nature Methods
    Volume: 22, P: 945-949

  • Dysregulated protein degradation drives diseases like cancer. Here, authors use protein language models to design target-binding peptides, which are subsequently attached to the catalytic domain of the OTUB1 deubiquitinase, generating “deubiquibodies” (duAbs). duAbs restore tumor suppressors and fusion oncoproteins, offering a programmable strategy for protein stabilization.

    • Lauren Hong
    • Tianzheng Ye
    • Pranam Chatterjee
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-10

  • Fusion oncoproteins drive paediatric cancers but are challenging to target due to their intrinsic disorder and lack of druggable pockets. Here, authors present FusOn-pLM, trained on FusOn-DB, which uses dynamic masking to outperform baselines in fusion-specific tasks and predict drug-resistant mutations, advancing therapeutic design.

    • Sophia Vincoff
    • Shrey Goel
    • Pranam Chatterjee
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-11