Routes a clash-free path between the two anchors, builds the linker extended, folds it on, then slides it into the nearest pocket that fits. Your structure never leaves this tab.
One PDB or mmCIF with every chain involved: both receptors and any ligand the anchors sit on.
Both fill every field from one published case: a D2R / NTS1R heterodimer bridged by a triazole–biphenyl–PEG linker. They differ only in PEG length — example 1 falls short, example 2 reaches, as the original study found.
Pick two attachment points. Either end can take either ligand.
* required. Typing offers the file's own chains, residues and atoms, best handles first.
Clash-free routes between the two atoms. The shortest is the minimum length any linker needs.
Select both atoms, then map the path.
| # | Points | Length Å | vs shortest |
|---|
Drag into the chain, or click to add at the end. Lengths are each piece's measured extended span.
| Chain | Span Å | vs route |
|---|
Reads top to bottom = left to right: the first piece is the end that meets atom 1, the last meets atom 2. Drag to reorder.
Blocks join to each other: acid + primary amine → amide; terminal alkyne + azide → 1,4-triazole. Blocks that cannot react stop the run.
Nothing is bonded to the protein; both directions are folded and ranked.
Keep this tab open: no server holds your place.
Map the path, choose a linker, then build.
| # | Points | Length Å | vs shortest |
|---|
One zip, in a folder of this name: every route, every placement, and a summary table.
LinkerBuilder 3D is a free web page that checks whether a chemical linker can bridge two ligands in a 3D structure. You give it one PDB or mmCIF file with two ligands bound in two receptors, and pick one atom on each ligand. It finds the clash-free routes between those two atoms through the structure, builds the linker you chose, folds it onto the routes and tells you whether it fits. It is aimed at bivalent ligands: two pharmacophores joined by a linker, each binding its own receptor.
The answer comes first, as a scale: No, Maybe · short, Probably OK or Yes, with the numbers behind it: the straight-line distance between the atoms, the shortest clash-free route, the linker’s extended length and how many placements arrive clash-free. The routes and the placements open in 3D, and one zip holds every route, every placement and a summary table.
Your structure stays in your tab. A Python engine (about 22 MB the first time, then cached) runs on your own processor, and the molecules are not sent anywhere. The only thing the page sends is an anonymous count of page openings, results and downloads, with the visitor’s country, as the footer says.
It is a feasibility check, not a prediction. It uses one conformer and does not judge strain, entropy or chemistry. A Yes means a clash-free placement arrives and the linker is longer than every route of the corridor; it does not mean the compound can be made, will bind or will be active.
The five Python modules that do the work are served as plain text, so you can read the code that ran on your structure. The page bundles open-source libraries under their own licences: Pyodide (MPL-2.0), NumPy, networkx (BSD), pysmiles (Apache-2.0), 3Dmol.js and JSME (BSD-3-Clause), JSZip and SmilesDrawer (MIT). Version 0.39.5.
Can this linker bridge these two anchor atoms, in this structure? The verdict is read against the corridor of clash-free routes between the atoms (the routes up to 10 Å longer than the shortest). Roughly: No when the linker is shorter than the shortest route and no placement arrives; Maybe · short up to the middle of the corridor; Probably OK from the middle to its far end; Yes beyond the longest route, when it arrives clash-free. When it falls short, the page says about how many PEG units would close the gap.
One PDB or mmCIF file that holds both receptors and the two ligands; one anchor atom on each ligand (the page ranks candidate pairs and suggests one); and a linker. The linker can be assembled from a shelf of ready-made pieces (PEG spacers, bivalent scaffolds and more), from a piece you draw or build from menus, or from a pasted list of SMILES, and the Auto mode searches chains of the pieces you tick. Two worked examples load from buttons: a linker that is too short and one that is long enough.
No molecule data leaves your browser. The file is read in your tab and a Python engine (Pyodide) runs the calculation on your own processor, so the page needs no server for it. After the page and the engine have loaded, the only request the page makes is the anonymous count described in the footer. Download what you want to keep: nothing is saved for you.
Whether the compound can be made, will bind or will be active. The check places one extended conformer on the routes and takes the receptors as they are in your file. A placement counts as arriving when each end of the linker is within 1 Å of its bonding point, clash-free. A No means this linker does not reach between these two atoms in this structure; it says nothing about other linkers or other conformations of the proteins.
Barbeau X. LinkerBuilder 3D 0.39.5. https://linkerbuilder3d.com/. Accessed (the date you used it). There is no DOI yet.