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Showing 1–4 of 4 results
Advanced filters: Author: Nawar Malhis Clear advanced filters

  • Although many proteins function by toggling between distinct conformations, most structure predictors remain limited to a single static fold. Here, the authors test the performance of AlphaFold2, AlphaFold3, and recent variants on a dataset of autoinhibited proteins exhibiting at least two functionally distinct conformations, and show that AlphaFold2 fails to reproduce the experimental structures of many autoinhibited proteins, but that it can capture conformational diversity when using uniform multiple sequence alignment subsampling.

    • Brooks H. Perkins-Jechow
    • Juan Pablo Iglesias Ahualli
    • Jörg Gsponer
    ResearchOpen Access
    Communications Chemistry
    Volume: 8, P: 1-13

  • Information on protein sequence variability and conservation can be leveraged to identify functionally important regions. Here, the authors develop new conservation measures that exploit taxonomy distances and LIST, a tool for predicting deleteriousness of human variants.

    • Nawar Malhis
    • Steven J. M. Jones
    • Jörg Gsponer
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-8

  • This Tutorial provides guide for how to evaluate, select and use publicly available computational tools for predicting intrinsic disorder in proteins, with a focus on performance and ease of use results, exemplified using results from the Critical Assessment of protein Intrinsic Disorder prediction experiment.

    • Lukasz Kurgan
    • Gang Hu
    • Zsuzsanna Dosztányi
    Reviews
    Nature Protocols
    Volume: 18, P: 3157-3172

  • Results are presented from the first Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment, a community-based blind test to determine the state of the art in predicting intrinsically disordered regions in proteins.

    • Marco Necci
    • Damiano Piovesan
    • Silvio C. E. Tosatto
    ResearchOpen Access
    Nature Methods
    Volume: 18, P: 472-481