[HTML][HTML] Computational design of vaccine immunogens

KM Castro, A Scheck, S Xiao, BE Correia - Current opinion in …, 2022 - Elsevier
Computational protein engineering has enabled the rational design of customized proteins,
which has propelled both sequence-based and structure-based immunogen engineering …

[HTML][HTML] Accurate de novo design of membrane-traversing macrocycles

G Bhardwaj, J O'Connor, S Rettie, YH Huang… - Cell, 2022 - cell.com
We use computational design coupled with experimental characterization to systematically
investigate the design principles for macrocycle membrane permeability and oral …

[HTML][HTML] Glycan masking in vaccine design: Targets, immunogens and applications

CE Martina, JE Crowe Jr, J Meiler - Frontiers in Immunology, 2023 - frontiersin.org
Glycan masking is a novel technique in reverse vaccinology in which sugar chains (glycans)
are added on the surface of immunogen candidates to hide regions of low interest and thus …

[HTML][HTML] Antigen-and scaffold-specific antibody responses to protein nanoparticle immunogens

JC Kraft, MN Pham, L Shehata, M Brinkkemper… - Cell Reports …, 2022 - cell.com
Protein nanoparticle scaffolds are increasingly used in next-generation vaccine designs,
and several have established records of clinical safety and efficacy. Yet the rules for how …

[HTML][HTML] Mannose-binding lectin and complement mediate follicular localization and enhanced immunogenicity of diverse protein nanoparticle immunogens

BJ Read, L Won, JC Kraft, I Sappington, A Aung, S Wu… - Cell reports, 2022 - cell.com
Nanoparticle (NP) vaccine formulations promote immune responses through multiple
mechanisms. We recently reported that mannose-binding lectin (MBL) triggers trafficking of …

De novo design of monomeric helical bundles for pH‐controlled membrane lysis

N Goldbach, I Benna, BIM Wicky, JT Croft… - Protein …, 2023 - Wiley Online Library
Targeted intracellular delivery via receptor‐mediated endocytosis requires the delivered
cargo to escape the endosome to prevent lysosomal degradation. This can in principle be …

[HTML][HTML] Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

M Ertelt, VK Mulligan, JB Maguire… - PLOS Computational …, 2024 - journals.plos.org
Post-translational modifications (PTMs) of proteins play a vital role in their function and
stability. These modifications influence protein folding, signaling, protein-protein …

Combining Rosetta Sequence Design with Protein Language Model Predictions Using Evolutionary Scale Modeling (ESM) as Restraint

M Ertelt, J Meiler, CT Schoeder - ACS Synthetic Biology, 2024 - ACS Publications
Computational protein sequence design has the ambitious goal of modifying existing or
creating new proteins; however, designing stable and functional proteins is challenging …

[HTML][HTML] Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

J Koehler Leman, S Lyskov, SM Lewis… - Nature …, 2021 - nature.com
Each year vast international resources are wasted on irreproducible research. The scientific
community has been slow to adopt standard software engineering practices, despite the …

[HTML][HTML] A versatile Halo-and SNAP-tagged BMP/TGFβ receptor library for quantification of cell surface ligand binding

J Jatzlau, W Burdzinski, M Trumpp, L Obendorf… - Communications …, 2023 - nature.com
TGFβs, BMPs and Activins regulate numerous developmental and homeostatic processes
and signal through hetero-tetrameric receptor complexes composed of two types of …