gRNAde MCP Server

# Default RNA Design Configuration for gRNAde MCP # Based on the original design.yaml from gRNAde ################################## # Target Structure Configuration ################################## # Path to target 3D structure (PDB format) # Will be provided via MCP tool parameters pdb_filepath: null # Target secondary structure in dot-bracket notation # Pseudoknots are supported using additional bracket types: [], {}, <> # Will be provided via MCP tool parameters target_sec_struct: null # Partial sequence constraints (hard constraints) - optional # Use '_' for designable positions and 'A', 'G', 'C', 'U' for fixed positions partial_seq: null ################################## # Design Mode Configuration ################################## # Design mode: '3d' (condition on 3D structure) or '2d' (condition on 2D structure only) mode: "3d" ################################## # Sampling Configuration ################################## # Total number of sequences to generate (default for quick operations) total_samples: 1000 # Number of sequences to sample per batch n_samples: 32 # Number of designs that pass filtering threshold n_pass: 100 # Minimum sampling temperature (lower = more conservative) temperature_min: 0.1 # Maximum sampling temperature (higher = more diverse) temperature_max: 1.0 # Filtering metric for initial design selection filter_metric: "openknot_score" # Threshold for filtering designs pass_threshold: 80 ################################## # Output Configuration ################################## # Output directory (will be set by MCP) output_dir: "results" ################################## # Model Configuration ################################## # Path to gRNAde checkpoint (relative to repo directory) model_path: "checkpoints/gRNAde_drop3d@0.75_maxlen@500.h5" # Model architecture parameters node_in_dim: [15, 4] node_h_dim: [128, 16] edge_in_dim: [132, 3] edge_h_dim: [64, 4] num_layers: 4 drop_rate: 0.5 out_dim: 4 ################################## # Featurizer Configuration ################################## radius: 0.0 top_k: 32 num_rbf: 32 num_posenc: 32 max_num_conformers: 1 noise_scale: 0.1 drop_prob_3d: 0.75 ################################## # System Configuration ################################## seed: 42 gpu: 0