4. Project Types for Computational Protein Design

4.1 De Novo Miniprotein Design with BindCraft

Ariax Bio's flagship project type leverages the BindCraft platform for de novo computational design of miniproteins that bind your specified target.

What are De Novo Miniproteins?

A de novo miniprotein is a small protein—typically below 15 kDa in molecular weight—that is 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. The term "de novo" itself means "from the beginning" or "new," and in the context of protein design, it refers to building a protein sequence and structure without relying on any natural templates.

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 Future Types: mAb, VHH, Peptide, 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.
• Peptide: Short chains of amino acids (10-30 amino acids) that can bind to targets with pharmacology more similar to small molecules than biologics.

Is there a protein design tool you would like to see hosted at Ariax Bio? Let us know at info@ariax.bio.