4. Project Types for Computational Protein Design
Ariax Bio leverages the BindCraft platform for de novo computational design of protein binders that target your specified protein. BindCraft supports two main project types: miniprotein and peptide design. Learn more about why BindCraft is revolutionizing protein design in our detailed analysis.
4.1 Miniprotein
De novo miniprotein design creates small proteins—typically 65-150 amino acids (below 15 kDa in molecular weight)—that are designed entirely from scratch using computational methods. Unlike traditional protein engineering, which modifies existing natural proteins, de novo design creates new amino acid sequences and structures not found in nature.
Miniproteins are notable for their compact size and their ability to form stable, well-defined three-dimensional structures. Their small size makes them easier to produce and highly stable, which is advantageous for both research and therapeutic applications. Because of these properties, de novo miniproteins are highly modular and can be tailored for specific structural or functional goals, such as binding to a particular target.
The benefits of de novo miniproteins are wide-ranging. They hold significant therapeutic potential, serving as agents for various diseases, including use as recombinant biologics, components of engineered cell therapies, lipid nanoparticles, and viral gene delivery platforms. Additionally, these proteins can act as building blocks for new biomaterials and, owing to their specificity, are valuable reagents for a variety of applications in biochemistry, molecular biology, and cell biology.
4.2 Peptide
Peptide design focuses on short amino-acid chains (8–30 residues) that sit between small molecules and full-length proteins in both size and complexity. Designed peptides can engage surfaces that are hard to reach with traditional small molecules while remaining inexpensive to synthesise and easy to chemically modify. They are useful as research probes or as starting scaffolds for therapeutic optimisation, but typically require additional engineering to achieve the stability and affinity offered by larger protein scaffolds.
4.3 Future Types: mAb, VHH, etc.
With the rapid pace of protein design research, we anticipate supporting future open-source platforms as they become available for:
- mAb (Monoclonal Antibody): The most prevalent modality used in biologic-based therapies. Structurally, mAbs are large (150 kDa) Y-shaped glycoproteins composed of two heavy and two light chains, exhibiting high specificity and affinity for their target antigens.
- VHH (Nanobody): Small, single‑domain antibodies (~15 kDa) derived from camelid species that can often bind epitopes that are inaccessible to conventional antibodies.
Is there a protein design tool you would like to see hosted at Ariax Bio? Let us know at info@ariax.bio.