abYdraw draws antibody and T-cell receptor formats. Everything you draw is also written out as AbML, a short text description of the molecule, and the two always match: change one and the other follows.
Draw your first antibody in one minute
- Press Clear canvas at the top left to start empty.
- Press these buttons in order: VH, CH1, H, CH2, CH3. Each one adds a domain onto the end of the chain, going from the N-terminus down to the C-terminus. That is one heavy chain.
- Click on blank space in the drawing to deselect, then press VL and CL. That is one light chain.
- Press Copy chain twice, once with a heavy-chain domain selected and once with a light-chain domain selected. You now have four chains.
- Press Auto-pair. The domains that belong together find each other and the whole IgG falls into shape.
Faster still: press Format library at the top of the page, pick one of the forty ready-made formats, and change it.
Adding and removing domains
The grey line under Build always tells you where the next domain will go. With a domain selected it is added just after that domain; with nothing selected it starts a new chain.
- Click a domain to select it. The selected one has a thick blue outline, and its text lights up in the AbML box.
- Insert before and Insert after, on the right, put a domain anywhere in a chain rather than only at the end.
- Delete, or the Delete key, removes the selected domain.
- Undo and Redo in the toolbar, or Ctrl+Z, step back through any change, including clearing the canvas.
Joining domains together
Two kinds of join matter. Along a chain, domains are simply next to each other. Across chains, domains pair: VH with VL, CH3 with CH3, and so on.
- Auto-pair does the obvious ones for you and can be pressed as often as you like.
- For anything unusual, select a domain, press Pair with another domain, then click its partner. Clicking a current partner unpairs them instead. Esc cancels.
- Disulfides is the number of disulfide bonds between a domain and its partner. They are drawn as gold bars.
- A linker (the L button) is a flexible stretch drawn as a dashed line. Add a
LENGTH comment with a number of amino acids and the drawn linker grows to match.
- A hinge (H) is the thick bend between the arms and the stem of an antibody.
Targets, modifications and drugs
- Specificity is a letter that says which target a binding site is for. All the domains of one arm share a letter. Two letters, such as
ab, mean a domain that binds both. Each letter gets its own colour.
- To name the target, add a comment with the keyword ANTI and the target's name, for example
ANTI:HER2. It appears beside the domain and in the summary.
- Modification buttons mark a domain: positive or negative charge for steering chain pairing, knob and hole which are drawn as a bump and a matching notch, not glycosylated to remove the sugar from a CH2, and general modification for anything else, which you then explain with a
MOD or NOTE comment.
- Drug payloads adds a drug to that domain, drawn as a pink star on a short tether. Any domain can carry one, including linkers and hinges, and a domain can carry several. For random, non-specific conjugation instead, add a final chain
[ADC] in the AbML box.
Moving things around
Nothing is drawn at fixed coordinates. The domains push and pull on each other until the format settles, so a new design arranges itself.
- Drag any domain to move it. It stays where you drop it, shown by a small blue dot. Double-click it to let go, or press Release pins for all of them.
- Relax nudges the layout again. Re-layout throws the arrangement away and starts over. Fit re-centres the view.
- Drag blank space to pan, and scroll to zoom.
- Labels, Comments and Glycans turn those parts of the picture on and off.
Reading the picture
The full key is at the bottom right of the page. In short: variable domains have three loops drawn at the binding end, which always points outwards; light-chain domains are the paler shade of their colour; T-cell receptor domains have cut-off corners, a hatched fill and an inner outline, so they stand apart from antibody domains even in a black-and-white print; hexagons are other protein domains (X) or chemical cross-linkers (C); gold bars are disulfides; dashed lines are linkers; pink stars are drugs.
The AbML box
You never have to type AbML, but it is worth knowing how to read it. VH.a(1:6) means a heavy variable domain, binding target a, numbered 1, paired with domain 6. Dashes join domains along a chain, a vertical bar separates chains, curly brackets count disulfides and square brackets hold comments.
- Typing in the box redraws the molecule as you go. Mistakes are underlined in red and explained underneath; the drawing keeps showing the last good version until you fix it.
- Tidy renumbers everything neatly. Copy puts the text on the clipboard, which is the easiest way to send a format to a colleague.
- Your work is kept in this browser, so the page comes back as you left it.
Saving a picture
Save SVG gives a sharp vector file for figures and slides, and it keeps the AbML inside it. Save PNG gives an image file for documents and email. Both are saved at the current arrangement, so tidy the layout first.