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  1. Machine learning-based prediction of peptide aggregation during chemical synthesis

    Publication
    Solid-phase peptide synthesis enables the study of countless peptides, but aggregation during synthesis hinders production of many sequences of interest. Now, machine learning models enable prior identification …

  2. The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design

    Publication
    Although canonical protein design has benefited from machine learning methods trained on databases of protein sequences and structures, synthetic heteropolymer design still relies heavily on physics-based methods …

  3. Heuristic energy-based cyclic peptide design

    Publication
    Rational computational design is crucial to the pursuit of novel drugs and therapeutic agents. Meso-scale cyclic peptides, which consist of 7-40 amino acid residues, are of …

  4. CyclicCAE: A Conformational Autoencoder for Efficient Heterochiral Macrocyclic Backbone Sampling

    Publication
    Macrocycles are a promising therapeutic class. The incorporation of heterochiral and non-natural chemical building-blocks presents challenges for rational design, however. With no existing machine learning methods …

  5. A robust and versatile computational peptide design pipeline to inform wet-lab experiments

    Publication
    Since Merrifield’s development of solid-phase peptide synthesis, we have seen explosive growth in the number of synthetic building-blocks that can be incorporated into peptides. This …

  6. Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

    Publication
    Post-translational modifications (PTMs) of proteins play a vital role in their function and stability. These modifications influence protein folding, signaling, protein-protein interactions, enzyme activity, binding affinity …

  7. How to Design Peptides

    Publication
    Novel design of proteins to target receptors for treatment or tissue augmentation has come to the fore owing to advancements in computing power, modeling frameworks, and translational successes …

  8. Multibody molecular docking on a quantum annealer

    Publication
    Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of …

  9. Accurate de novo design of membrane-traversing macrocycles

    Publication
    We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6–12 residue macrocycles …

  10. Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites

    Publication
    Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this …

  11. MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform

    Publication
    As non-“self” macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off therapy, or even cause life-threatening reactions …

  12. 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 …

  13. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

    Publication
    The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades …

  14. Computational design of mixed chirality peptide macrocycles with internal symmetry

    Publication
    Cyclic symmetry is frequent in protein and peptide homo‐oligomers, but extremely rare within a single chain, as it is not compatible with free N‐ and C‐termini …

  15. 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 …

  16. Designing Peptides on a Quantum Computer

    Publication
    Although a wide variety of quantum computers are currently being developed, actual computational results have been largely restricted to contrived, artificial tasks. Finding ways to apply quantum computers …