CYJ: Non-Canonical Zn2+-Binding Site Prediction Server

Help page and short user guide

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This page explains how to prepare input files, submit a job, and interpret the output of CYJ server. It is intended as a quick guide for first-time users.

Tip: If you are using the server for the first time, start with the example workflow below.

Quick start

  1. Prepare your input file in mmCIF format.
  2. Upload the file.
  3. Set the chain identifier.
  4. Submit the job and wait for processing to finish.
  5. Inspect the result with visualization output.

Input requirements

Accepted input

  • Protein structure file in mmCIF format
  • Chain ID for analysis

Please check before upload

  • The file is a valid mmCIF file
  • The chain ID exists in the uploaded structure
  • The structure contains standard residue numbering

Example workflow

A typical analysis starts by uploading a protein structure mmCIF file and specifying the target chain. After submission, the server processes the structure and returns a result page with predicted residues and an interactive 3D viewer.

Predicted residues are displayed as clickable labels such as His17 (0.56). Clicking a residue label moves the viewer to that residue and highlights it in the structure.

Output interpretation

Predicted residue list

The server reports predicted residues in a compact button format. Each residue label includes residue name, residue number, and the score.

3D structure viewer

The protein is shown as a cartoon model with wireframed atoms, while predicted residues are highlighted in ball-and-stick representation in red. Clicking a listed residue on the right focuses the viewer on that site.

Output

  • Interactive 3D structure visualization
  • A list of predicted residues

Frequently asked questions

Why does the structure viewer not load my mmCIF file?

Some structures may not load directly in the browser viewer. In such cases, the server may automatically convert the structure to PDB format and continue visualization using the converted file.

Why do I get no predicted residues?

This may occur if the selected chain is incorrect, the uploaded file is malformed, or the structure does not satisfy the assumptions of the prediction pipeline.

Can I use the output in publications?

Yes, but please verify the predictions independently and cite the corresponding manuscript describing the server.

Contact

For questions, bug reports, or suggestions, please contact: yura.kei@ocha.ac.jp