Use NeuroBind

NeuroBind is a compute-intensive model. Typical runtimes average around 12 hours, but larger or more complex targets may require multiple days to complete.

Hotspots allow you to guide NeuroBind to focus binding interactions on specific regions of your target. These are typically known or desired binding sites—such as epitopes or functional surfaces—that you want the designed binder to interact with. In the context of antibody design, hotspots can be thought of as the ideal epitope region within the target.

Each hotspot is defined on a separate line using the following format:

SEQ_ID:RES_ID

• SEQ_ID → The name of the target sequence containing the hotspot.
• RES_ID → The residue index (1-based) within that sequence.

🔹 Example Input:

Protein_1:6
Protein_1:7
Protein_2:26
Protein_2:28

⚠️ Notes:

• Sequence names must match those provided in Target Sequences.
• Residue indices are 1-based (i.e., the first residue is 1, not 0).
• You can provide one or more hotspots depending on your design goals.

Custom templates allow you to specify a reference structure for the binder you wish to design. This can be:

• An existing binder (e.g., antibody, peptide, nanobody, scFv) you’d like to refine, akin to affinity maturation.
• A novel scaffold (e.g., miniproteins, DARPins, or other engineered proteins).

Ensure uploaded templates are high quality (e.g., well-resolved PDBs), protein-only, and gap-free. Remove non-protein elements such as nucleotides, heteroatoms, or waters.

Paratopes (Optional)

Paratopes define the residues within your template that should drive the interaction with the target structure (similar to specifying the CDRs for antibodies). They are optional, but specifying them can improve accuracy and focus during design.

Each paratope is specified on its own line in the format:

CHAIN_ID:RES_ID

• CHAIN_ID → Chain ID from the uploaded structure (e.g., A, H, L).
• RES_ID → 1-based residue index (e.g., 1, 25, 102).

🔹 Example Input:

A:6
A:7
B:26
B:28
L:49
H:32

⚠️ Notes

• Indices are 1-based (the first residue is 1, not 0).
• You may provide one or more paratopes.
• Paratopes are only used if a Custom Template is uploaded.
• Sequence should match chain IDs and residue indices exactly as found in the PDB file.