AlphaLasso: Lassos in AlphaFold generated structures

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.

Project name:

Email:

Input data format:

cif|cif.gz format
pdb format
Multiple chains
cif|cif.gz|pdb format

Select datafile in file format:

Select datafiles in cif|cif.gz|pdb file format

Use the CTRL/CMD key to select multiple files.

Download and submit :

Recompute structure from database:

Calculate:

Loop closing bridge:

Loops list:

Begin:

End:

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

Closing aminoacids:

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

Bridge type:

Disulfide Ionic Covalent (non-disulfide) All

Number of random closures (10-100):

Bridge length:

Min:

Max:

Search for identical structures:

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.

Lasso
Multimodel
No lasso

Single chain input: cif|cif.gz file format

Single chain input: pdb file format

Multimodel cif|cif.gz|pdb file format

Input and output information