How do I identify the quality of the structure in the lasso region of interest?
The quality of the structure can be verified using several metrics. On each protein page, there is a deep lasso pLDDT metric, which describes the average quality of the whole lasso structure. After selecting the show shallow lasso option, the metric will also account for shallow crossings. User-submitted or recomputed structures also feature an artifact check page, where pLDDT metrics for loop and both tails can be found. A comprehensive overview of the structure’s quality is available in the Mol* viewer utilizing the pLDDT color scheme.
What is the difference between deep and shallow lasso?
Shallow (non-deep) crossings are those that are less than 3 residues from a chain terminus or a loop, or less than 10 residues from another crossing. Deep lasso is a lasso that has at least one deep crossing. For more, check https://alphalasso.cent.uw.edu.pl/lasso_detection#reduction.
You can use different values to specify the shallow lasso when using the server as well as while recomputing the existing structure from the database.
What is a supercoiling / a supercoiled lasso?
Supercoiling happens when a tail winds around a loop and crosses a loop from the same side (at least) twice in a row. Supercoiled lassos are denoted with LS instead of L.
What is the meaning of lasso symbols like L+4C or LS4-+--C
We divide lassos into four types:
One-sided:
Non-supercoiled: L1, L2, L3, ...
Supercoiled: LS2, LS3, LS4, ...
One-sided lassos are pierced by only one tail, which can be specified by an additional "N" or "C" behind a number, e.g., L2N, L4C.
Two-sided:
Non-supercoiled: LL1,1, LL1,3, LL4,2, ...
Supercoiled: LSL2,1, LLS1,3, LSLS4,2, ...
In case of two-sided lassos, the number before the comma refers to the N-tail, and the number after the comma refers to the C-tail. LSL means that the N-tail supercoils, LLS that the C-tail supercoils, and LSLS that both tails supercoil.
You can check some examples here: https://alphalasso.cent.uw.edu.pl/lasso_classification.
Additionally, we distinguish loop sides, which induces crossing orientations: + and - (check https://alphalasso.cent.uw.edu.pl/lasso_detection#piercing). Therefore, the lasso type can be even more specific, by adding a sequence of + and - behind a number, e.g., LSLS3++-,2--. Note that consecutive tail piercings of a non-supercoiled lasso must alternate; therefore, to shorten the notation, we leave only the first sign (and we keep it before the number), e.g., L3+-+ is the same as L+3.
What is a GLN matrix, and how to interpret it?
Gauss Linking Number matrix is an alternative method of lasso type detection. It requires a computation of the Gauss Linking Integral between a loop and every possible continuous subchain of a tail. After the computation, Gauss Linking Integral values are represented on a matrix-map, where each value is placed at matrix coordinate (x,y)=(subchain beginning, subchain ending). You can read more about this method in the article: https://www.nature.com/articles/s41598-020-71874-2.
Can I process multiple files/models at once?
Yes! On the job submission page in the Input data format, you can use the option under Multiple files and upload multiple files by holding the Ctrl or Cmd key while selecting your files. You can also upload a PDB file containing multiple models in the MODEL…ENDMDL blocks. Depending on the complexity of your structures, you can process 10-15 models in a single request.
I’m getting error messages when trying to process my structure. How can I fix that?
Make sure that your files are of correct mmCIF or PDB format and that they contain only a single chain with no gaps. Try using other tools to see if the problem persists. If you still cannot process the file, please contact our team. We will be happy to resolve your issue and improve the service for other users.
Is there a way to improve the speed of the analysis?
You can selectively turn off some features, which will improve the calculation speed. The most time-consuming is the identity search; if you don’t need to look up similar structures, you can turn this feature off during submission.
