AlphaLasso

Examples: A0A067QHV7, FJHX, HUMAN, L2, Titin

AlphaLasso

The AlphaLasso database compiles data on lassos within protein models solved by AlphaFold. It identifies loops closed by cysteine 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, individuals can utilize the server to analyze their own protein structures predicted by AlphaFold, employing the same methodology.

AlphaLasso has identified more than 3 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 All 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).

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.

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