openfree PRO

Hi, can you please explain how your model handles cooperativity and allostery in protein design, where the interactions between amino acids can give rise to emergent properties that aren't simply the sum of their individual contributions?

cooperativity and allostery are handled in the following ways:

Structural Interaction Modeling:

The protein_diffusion_model function considers the entire protein structure and models amino acid interactions through a diffusion process
The parameters helix_bias, strand_bias, and loop_bias control interactions between secondary structure elements

Integration of Physicochemical Properties:

Hydrophobic/hydrophilic interactions are considered through hydrophobic_target_score and hydrophobic_potential
Local interactions are controlled by adjusting specific amino acid distributions using aa_bias and aa_bias_potential

Dynamic Optimization:

Structure is gradually optimized through a 25-step diffusion process (num_steps="25")
Cooperative interaction effects are evaluated by monitoring structural stability through plddt_plot

Multi-scale Analysis:

The analyze_prompt() function identifies high-level functional requirements
These are translated into low-level structural parameters by the extract_parameters() function
The calculate_similarity() function references characteristics from similar structures

Through this comprehensive approach, the model implements emergent properties in the overall protein structure rather than simply summing individual amino acid characteristics.