OTeam-AI4S/ODesign

What it solves

ODesign is an all-atom generative world model designed for biomolecular interaction design. It allows scientists to create diverse classes of binding partners (proteins, ligands, nucleic acids, and cyclic peptides) for arbitrary targets by specifying epitopes or hotspots on the target molecule, providing fine-grained control over the design process.

How it works

ODesign uses a generative model that can operate in different design modes (flexible or rigid receptor) across multiple modalities. It takes a reference structure and a specification of hotspot residues or atoms as input and generates a binding partner. The system includes an inverse-folding module (OInvFold) to determine the sequence for the generated backbone structures. It also supports "partial diffusion," which allows users to modify specific regions of an existing binding molecule to improve its properties.

Who it’s for

This tool is intended for computational biologists, chemists, and pharmaceutical researchers who need to design new biomolecules that can bind to specific targets for drug discovery or protein engineering.

Highlights

• All-to-all design: Supports generating proteins, ligands, nucleic acids (DNA/RNA), and cyclic peptides.
• Multi-modal capabilities: Specific pre-trained models for different modalities (e.g., odesign_base_prot_flex for proteins).
• Fine-grained control: Users can specify exact hotspots on target molecules to guide the generation.
• Versatile design tasks: Includes protein-binding protein/ligand design, atom and motif scaffolding, and nucleic acid backbone generation.
• Partial Diffusion: Ability to modify existing molecules rather than generating them from scratch.