bio_tools 0.1.1

Install, run, and inspect computational biology and chemistry tools, e.g. AlphaFold, Boltz, RFdiffusion, and ProteinMPNN
Documentation 
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{
  "fields": [
    {
      "name": "job_name",
      "label": "Job name",
      "kind": "text",
      "default": "mber-demo",
      "required": false,
      "help": "",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "target_pdb",
      "label": "Target antigen PDB",
      "kind": "file",
      "default": "HEADER    PASTE A TARGET ANTIGEN PDB HERE",
      "required": true,
      "help": "",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": ".pdb,.ent,.cif",
      "task": ""
    },
    {
      "name": "target_chains",
      "label": "Target chains",
      "kind": "text",
      "default": "A",
      "required": true,
      "help": "Comma-separated if the target is bound across more than one chain, for example A,B.",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": 20,
      "accept": "",
      "task": ""
    },
    {
      "name": "hotspots",
      "label": "Epitope hotspots (optional)",
      "kind": "text",
      "default": "A56",
      "required": false,
      "help": "Comma-separated target residues, for example A56,A57. Empty lets mBER bind anywhere on the target.",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "num_accepted",
      "label": "Designs to keep",
      "kind": "number",
      "default": 10,
      "required": false,
      "help": "The run stops once this many trajectories have passed the iPTM/pLDDT filters.",
      "options": [],
      "rows": null,
      "minimum": 1,
      "maximum": 1000,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "max_trajectories",
      "label": "Trajectories to attempt",
      "kind": "number",
      "default": 1000,
      "required": false,
      "help": "Upper bound on attempts if num_accepted is never reached.",
      "options": [],
      "rows": null,
      "minimum": 1,
      "maximum": 100000,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "min_iptm",
      "label": "Minimum iPTM",
      "kind": "number",
      "default": 0.75,
      "required": false,
      "help": "",
      "options": [],
      "rows": null,
      "minimum": 0.0,
      "maximum": 1.0,
      "step": 0.05,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "min_plddt",
      "label": "Minimum pLDDT",
      "kind": "number",
      "default": 0.7,
      "required": false,
      "help": "",
      "options": [],
      "rows": null,
      "minimum": 0.0,
      "maximum": 1.0,
      "step": 0.05,
      "maxlength": null,
      "accept": "",
      "task": ""
    }
  ],
  "tasks": []
}