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Structure prediction · Protein Design

OpenDDE

Run a protein, DNA/RNA, or ligand co-folding prediction.

Predict protein structure from nucleic acid or amino acid sequence. Predict the structure of ligands, nucleic acids, and ions, or complexes of these molecules. This is a relatively new, but very accurate model.

Documentation ↗ Home page ↗ Source code ↗
Input

Configure a small job

POST
Add one box per chain: Protein, Ligand, DNA, or RNA. Ligands take a SMILES string or a CCD_ code (e.g. CCD_ATP). A modification applies a CCD residue code at a given position; "Cyclic" bonds the chain's first and last residue.
One protein chain sequence per line.
One DNA chain sequence per line.
One RNA chain sequence per line.
JSON list of {"type": "protein"|"dna"|"rna", "chain": "A", "sequence": "..."}.
One ligand SMILES per line.
One ligand SMILES per line.
JSON list of covalent bonds between the chains above, e.g. [{"atom1Chain":"A","atom1Idx":"32","atom1Atom":"C","atom2Chain":"B","atom2Idx":"1","atom2Atom":"N"}]. Chains are lettered A, B, C... in the order entered: protein chains first, then DNA, then RNA, then ligands.
Comma-separated seeds, e.g. "101,102"; each produces an independent set of samples.
Ready
Response

JSON result

{
  "status": "Ready for a request"
}