An easy-to-use computational tool for predicting 3D properties of disordered proteins
Author:
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Molecular Biology,Biochemistry,Biotechnology
Link
https://www.nature.com/articles/s41592-023-02160-y.pdf
Reference5 articles.
1. Holehouse, A. S. & Kragelund, B. B. The molecular basis for cellular function of intrinsically disordered regions. Nat. Rev. Mol. Cell Biol. https://doi.org/10.1038/s41580-023-00673-0 (2023). This review article presents a systematic overview of how IDRs can drive cellular function.
2. Emenecker, R. J., Guadalupe, K., Shamoon, N. M., Sukenik, S. & Holehouse, A. S. Sequence-ensemble-function relationships for disordered proteins in live cells. Preprint at bioRxiv https://doi.org/10.1101/2023.10.29.564547 (2023). This preprint reports a novel method for the rational design of IDRs and then uses that method to explore how IDR sequence influences ensemble properties and molecular function in living cells.
3. Joseph, J. A. et al. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. Nat. Comput. Sci. 1, 732–743 (2021). This paper presents the coarse-grained model used to generate the training data for ALBATROSS.
4. Griffith, D. & Holehouse, A. S. PARROT is a flexible recurrent neural network framework for analysis of large protein datasets. eLife 10, e70576 (2021). This paper presents a general-purpose machine learning package that makes it easy to train models that map between amino acid sequence and some per-sequence or per-residue annotation.
5. Tesei, G. et al. Conformational ensembles of the human intrinsically disordered proteome. Nature https://doi.org/10.1038/s41586-023-07004-5 (2024). This work reports a complementary body of work using a different coarse-grained forcefield to simulate all IDRs in the human proteome.
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