This tutorial explains how to use ADNeX to search proteins, explore interaction evidence, inspect structures, and download datasets. Follow the steps below for a complete workflow from query to data export.
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1. Search for a Protein

• Open the home page and enter a gene symbol or UniProt ID in the Query protein box.
• Use autosuggestions to pick the correct target, then click Search.
• NOTE: If you query BIN1 or APOE families, select the variant prompt that matches your analysis goal.
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2. Read the Results Layout

• The left panel summarizes bait metadata and links to external resources.
  • Click the gene symbol to view detailed information about that gene on GeneCards.
• The center panel contains Network, Volcano, and Table tabs for interaction-level exploration.
• Network tab shows the interaction network for the selected bait.
• Volcano tab displays the significance versus effect size for interactions.
• Table tab provides a detailed list of interactions with sortable columns.
• The right panel provides AlphaFold3 structure, CRISPRi hit context, and brain-expression views.
• AlphaFold3 structure shows the predicted protein complex structure of selected interaction.
• CRISPRi hit context shows the effect of gene knockdown on the interaction network.
• Brain/Cell lines (HEK293 & HCT116) expression view displays the expression pattern of the gene in different brain regions.
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3. Results Exploration

• In both Network and Volcano tabs, use zoom controls to inspect dense neighborhoods. Double click the plot to reset the view. Hover on points to see details in the Volcano tab.
  Show GIF
• Switch volcano source between ADNeuronNet and Full to compare selective versus broad signal.
  Show GIF
• Click a point in volcano or a row in table to synchronize structure and expression context.
  • After selecting an interaction, the right panel will show AlphaFold Structure, CRISPRi hit context, and brain-expression views.
  • Use structure zoom controls to focus on interface regions.
  • Click Download CIF to save the current predicted interaction structure when available.
  Show GIF

4. Download Data

• Open Data in the header to access downloadable ADNeuronNet source datasets.
• Use card download buttons for full files; the Volcano card includes both Filtered and Full versions.
• Use external database links for HINT, OpenCell, BioPlex, BioGRID, and STRING reference downloads.

5. Tips and Troubleshooting

• If no structure appears, the selected interaction may not yet have a matched CIF file.
• Use UniProt-style IDs when symbol-based search is ambiguous.
• For data questions, reporting issues, or collaboration requests, use the Contact page.