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  1. Sequence-structure-function relationships in the microbial protein universe

    Publication
    For the past half-century, structural biologists relied on the notion that similar protein sequences give rise to similar structures and functions. While this assumption has driven research …

  2. Docking cholesterol to integral membrane proteins with Rosetta

    Publication
    Lipid molecules such as cholesterol interact with the surface of integral membrane proteins (IMP) in a mode different from drug-like molecules in a protein binding pocket. These …

  3. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

    Publication
    Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional …

  4. Specificities of modeling membrane proteins using multi-template homology modeling

    Publication
    Structures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the ProteinDataBank. Because of this disparity, methods for modeling …

  5. Structure-Based Protein Function Prediction using Graph Convolutional Networks

    Publication
    The large number of available sequences and the diversity of protein functions challenge current experimental and computational approaches to determining and predicting protein function. We present a deep …

  6. Macromolecular modeling and design in Rosetta: recent methods and frameworks

    Publication

  7. Better together: Elements of successful scientific software development in a distributed collaborative community

    Publication
    Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal …

  8. Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter

    Publication
    More than 80 loss-of-function (LOF) mutations in the SLC6A8 creatine transporter (hCRT1) are responsible for cerebral creatine deficiency syndrome (CCDS), which gives rise to a spectrum …

  9. Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

    Publication
    Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For …