Openfold3 Ob0 Tools#

Configuration File: remote_tools/openfold3_ob0_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the openfold3_ob0_tools.json configuration file.

Available Tools#

openfold3_ob0_fold (Type: RemoteTool)#

Predict an all-atom biomolecular structure with OpenFold3 0.5.0 and the OpenBind-0 parameters. Th…

openfold3_ob0_fold tool specification

Tool Information:

  • Name: openfold3_ob0_fold

  • Type: RemoteTool

  • Description: Predict an all-atom biomolecular structure with OpenFold3 0.5.0 and the OpenBind-0 parameters. The query is a list of chains, each with a molecule_type (protein, dna, rna or ligand) and a sequence – SMILES for a ligand. Returns the structure file paths, the per-sample confidence scores and timings; the mmCIF text itself is opt-in.

Parameters:

  • chains (array) (required) The chains of one complex.

  • seed (integer) (optional) Random seed; the same seed reproduces the fold.

  • num_diffusion_samples (integer) (optional) Structures to sample per seed (upstream’s default is 5). Each is scored separately, so this is how to compare conformations; rank them on scores.

  • num_model_seeds (integer) (optional) How many model seeds to run (default 1). Total structures is this times num_diffusion_samples.

  • return_structures (boolean) (optional) Return the mmCIF text (default false: megabytes). The per-sample ranking scores come back either way; the full per-residue confidence record is returned only when it is under 64 KiB, and scores_omitted names it otherwise.

Example Usage:

query = {
    "name": "openfold3_ob0_fold",
    "arguments": {
        "chains": ["item1", "item2"]
    }
}
result = tu.run(query)