Sharaf Lab

Structure · Figures · Notes

Lab tools.

Small browser-based utilities built by the Sharaf Lab. Files are processed on your own device and are never uploaded.

Check every result. These tools were vibe coded: built quickly with AI assistance and not independently validated. Compare their output with your own data and standard software before using it in figures, analyses or publications.

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Sequence · Domains · Topology · 3D

From sequence to topology.

Open one DSSP-processed CIF file to see its secondary structure residue by residue, find domains from the coordinates, draw a topology diagram, and view the chain in 3D. Every view uses the same domain colors, and each one downloads as a figure.

  1. Process your structure with DSSP first. Upload your .cif (or PDB) file to pdb-redo.eu/dssp and download the annotated mmCIF it returns.
  2. Open that DSSP-processed .cif file here. The sequence, domains, topology diagram and 3D view all read from it.

Sequence and secondary structure

Source code: NaimaSharaf/Second-Structure

Edit your picture

Select a letter to edit one residue, or enter a range in the current chain. Structure overrides change the drawing, not your source file.

No structure overrides.
Chain A
α-helix3₁₀ / π helixβ-strandLoop / turn / bend
Select a residue to inspect its position and structure. Use left and right arrow keys to move along the sequence.

Element labels use CIF identifiers: α1 means alpha helix 1; β1 · A means strand 1 in sheet A. Hover over a label for the full identifier. Edited assignments are marked “Edited”. Coils represent helices: α-helices (H) and 3₁₀ / π helices (G, I) use separate colors; arrows represent E strands and B bridges. Other assignments appear as lines. Wrapped segments continue onto the next row; arrows point toward the C terminus. This is a sequence schematic, not a 3D structure.

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Topology diagram

No file loaded Drag to move · click a loop to select it · click again or Esc to unselect · double-click or F to flip · arrow keys nudge · Delete hides
Click a helix, strand or loop to select it.

3D structure

No structure loaded Open a CIF file with atom coordinates to view the chain in 3D, colored like the diagram.

The 3D structure appears here.

Domains

Residue ranges use the file's label numbering; separate pieces with commas (e.g. 1–10, 71–164). Helices take the domain color; strands use a lighter tint.

Residues in each domain

One-letter sequence of each domain, in residue order, with one entry for each continuous piece. Residues that are not in any domain are listed last.


            

          



          


          

        

      


      

        

          
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PDF · Notes

            
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