Interactive Pipeline - Interactive Enzyme Platform

Step 1 · Do You Know The Substrate?

Workflow Path

Step 1 Summary

Choose whether you know the substrate identity first. The next step will tell you what kind of file to prepare.

`Known Ligand`: you know the substrate identity.
`Unknown Ligand`: you do not know the substrate identity.

Step 2 · Do You Have A Structure File?

Structure Source

Choose whether you only have sequence data or already have a structure file prepared.

Protein Sequence (FASTA) Required when you do not upload a structure file. Maximum 1000 amino acids per protein. The FASTA header and line breaks do not count; uploaded structures use the selected target chain.

Upload Structure File

No structure file selected

Accepted formats: `.pdb`, `.cif`, `.mmcif`. If you want to select substrate/cofactor residues from the file, the uploaded structure must already contain those ligand coordinates.

Target Protein Chain Recommended for multi-chain CIF complexes.

Original residue numbering and model indices

Enter Initial Fixed Sites using the original file numbers, including insertion codes (for example A:10A). Later stages use the model indices below. Missing residues are never assigned to a neighboring residue. The original structure and this mapping are kept in the project download.

Original residue	Model index	Amino acid

Uploaded Structure File

MSA Source

Keep the platform MSA workflow or continue with an externally generated MSA result.

The built-in platform workflow will be used for MSA retrieval and conservation analysis.

Step 2 Summary

Pick whether you are submitting a structure file or a FASTA sequence. The next step unlocks only after that primary input is ready.

If you already have a structure file, upload it here.
If you only have sequence, paste FASTA here.

Step 3 · Continue Here

Step 3 follows your answers above plus the uploaded-structure analysis facts. The route updates from user intent and detected residues together.

Answer the route question for the current Step 3 branch here.

Resolved Route

This section shows the route resolved from Step 1, Step 2, and the Step 3 structure-analysis outcome.

What file should I provide?

Answer the questions above to see the exact file requirement and the next action in this form.

Answer the questions to see the required file content.

Known Ligand Inputs

Unknown Ligand Cofactors

Non-Protein Anchor Detection

Upload a structure to detect non-protein anchors

If usable non-protein anchor residues are present, you can select them here for SC-only shell extraction. Leave them unchecked to keep the original P2Rank route.

No usable non-protein anchors detected yet. Upload a structure first, or continue with the default P2Rank route.

Fixed-Site Defaults

Initial Fixed Sites (Optional) These become the initial seed residues for the later site-annotation stage.

Preserved Sites Mode

Conservation threshold is adjusted later in the site-annotation interface after the profile is computed.