AlphaLasso

Examples: A0A067QHV7, FJHX, HUMAN, L2, Titin

The AlphaLasso web server searches for lassos within protein models solved by AlphaFold. It identifies loops closed by cysteine, amide, ester or thioester bridges, calculates the minimal surfaces enclosing these loops, and examines how polymer termini intersect these surfaces using Gaussian Linking Number (GLN), all while factoring in pLDDT confidence values. Moreover, the website hosts a database of loops closed by cysteine bridges predicted on all high confidence AlphaFold models.

AlphaLasso has identified more than 15 million loops within the AlphaFold protein models. You can conveniently visualize all the determined surfaces using the built-in PDBe Mol* viewer.

Learn more » Show Data

Input file should be in the standard CIF file format (https://en.wikipedia.org/wiki/Crystallographic_Information_File).

Input file should be in the standard PDB file format (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html).

Up to 10 files in CIF, CIF.gz or PDB format can be uploaded at once. These can be different models of the same structure (as in this example) or any other set of structures.

For detailed information on other options, see Analyze your structure.

For detailed information on the resulting plots and topological fingerprints, see How to interpret lasso data.

Use the CTRL/CMD key to select multiple files.

Begin:
End:

Define first and last index of residue for loop closing. The list will automatically extend to accomodate more loops.

Define aminoacids forming a bridge by their three letter code (e.g. TYR and TRP).

Disulfide bridge length:
Min:
Max:
Amide bridge length:
Min:
Max:
Ester bridge length:
Min:
Max:
Thioester bridge length:
Min:
Max:
Smoothing iterations:
Stable lasso:
Minimal distance between crossings:

Default: 10

Minimal distance between crossing and tail end:

Default: 3

Minimal distance between crossing and loop:

Default: 3

How to cite