Colabdesign Tools#

Configuration File: remote_tools/colabdesign_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the colabdesign_tools.json configuration file.

Available Tools#

colabdesign_design (Type: RemoteTool)#

Design a protein BINDER against a target structure with BindCraft’s binder-hallucination step on …

colabdesign_design tool specification

Tool Information:

  • Name: colabdesign_design

  • Type: RemoteTool

  • Description: Design a protein BINDER against a target structure with BindCraft’s binder-hallucination step on ColabDesign 1.1.3 and AlphaFold-Multimer v3. Give the target as PDB text, its chain, the binder length and optionally hotspot residues. No alignment is needed and no external service is contacted. One call is one trajectory (gradient-based sequence optimisation through the structure predictor): it returns the best binder sequence, whether the trajectory passed BindCraft’s own pLDDT gates, and the final confidence terms. Only the design step runs – no MPNN redesign, reprediction, relaxation or filtering. The first request of each (target residues, binder length, recycles) shape compiles for minutes.

Parameters:

  • target_pdb (string) (required) The target structure as PDB text (ATOM records). Crop it to the region around the binding site: target residues plus binder length may not exceed 400.

  • chain (string) (optional) Target chain id(s) in the PDB, e.g. ‘A’ or ‘A,B’.

  • binder_len (integer) (required) Length of the binder to design, in residues.

  • hotspot (string) (optional) Target residues the binder should contact, in BindCraft’s grammar: ‘56’, ‘31,33,57’, ‘A31,A33’ or ‘A1-10’. Omit for no hotspot.

  • seed (integer) (optional) Random seed for the trajectory.

  • name (string) (optional) A job name; it prefixes the design’s name.

  • num_recycles_design (integer) (optional) AlphaFold recycles per design step (BindCraft’s default is 1). Part of the compiled program, so changing it recompiles.

  • soft_iterations (integer) (optional) Stage-1 logit iterations (BindCraft default 75). Upstream hard-codes the first 50, so values below 50 are not accepted.

  • temporary_iterations (integer) (optional) Stage-2 softmax iterations (BindCraft default 45).

  • hard_iterations (integer) (optional) Stage-3 one-hot iterations (BindCraft default 5).

  • greedy_iterations (integer) (optional) Stage-4 PSSM semi-greedy iterations (BindCraft default 15).

  • return_structures (boolean) (optional) Return the design PDB text and the per-step trajectory (default false). Sequences and scores come back either way.

Example Usage:

query = {
    "name": "colabdesign_design",
    "arguments": {
        "target_pdb": "example_value",
        "binder_len": 10
    }
}
result = tu.run(query)