Frequently asked questions

Is a registration required?

No, SL2 is free for all users and no login is required.

Which web-browsers are supported?

Every modern web-browser that supports WebGL. To check the compatibility of your browser and further information see the NGL documentation.

How do I use the NGL viewer?

A complete documentation of the NGL viewer can be found here.

Do I have to install a plugin to use the NGL viewer?

No, the NGL viewer is based solely on browser technologies that are provided by every modern web-browser. Additional installations are not needed. Please make sure that you have updated your browser to the latest version.

WHAT is the PURPOSE of sl2?

SL2 can be used to interactively insert protein segments such as loops of 3 to 35 residues length into gaps of protein structures.

What has to be provided to start a search?

The user has to upload a protein and specify the sequence of the destined segment and the two stem residues of the gap where the segment has to be inserted.

I get no results, what might be the problem?

In some rare cases (too long or too short sequences for the given stem distance) no suitable loops can be found. Try to extend the loop search by one amino acid in C- or N-terminal direction.

Why are the sequence and the stems not further enlonged?

In this case the end of the protein chain is reached. Try to enlong in the other direction.

What does the color range stand for?

The different colour schemes range from its min to its max value.
Clash scheme: white (no clashes) to orange to red (many)
SequenceID scheme: dark green (high) to light green (low)
Score scheme: green (high score --> better results) to blue (medium) to purple (low)

When is a clash considered as a clash?

A clash is counted as a clash if the backbone atoms overlap within 3 A.

Can the completed structure be downloaded from the server?

As soon as a suitable fragment is found and selected by the user, the structure can be downloaded with the inserted fragment which sequence is automatically mutated to the destined sequence provided by the user.

Are the sidechains of the loop included?

We add sidechains in a standard configuration. These might lead to clashes. Please have in mind that an energy minimization might be necessary before further usage of the model.

What is included in the different download files?

All found loops can be downloaded in a single PDB-file where the individual loops are separated by a model tag.
A single loop can be downloaded renumbered and inserted at the correct position in the user-provided structure file.

How often will the database been updated?

The Database will be updated at least every three month.