AptamerDesigner V7
Design DNA aptamers against any protein target using the V7 transformer model.
The model was trained on 70,876 protein-DNA binding pairs and evaluates:
binding_score— model-predicted binding affinitymfe— minimum free energy of the aptamer fold (ViennaRNA)g4_score— G-quadruplex propensitystem_fraction— fraction of nucleotides in stemsbalanced_score— composite ranking score
No installation required. Model weights run entirely on the server.
Select a pre-configured APOBEC3 target. Protein embeddings are pre-loaded — no FASTA upload needed.
Target protein
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Designed Aptamers
How to use Custom Target
- Paste your protein in FASTA format (single sequence)
- Provide interface residue positions — the residue indices (0-indexed from the sequence start) that define the binding site (e.g. active-site residues, catalytic loops, zinc-coordinating residues)
- Adjust design parameters and click Design Aptamers
Tip: Interface positions come from structural analysis (PDB), mutagenesis data, or literature on your protein's active site.
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Designed Aptamers
Model: AptamerScorerV7 · 28M parameters · Trained on 70,876 protein-DNA pairs**