Frequently Asked Questions (FAQ) - Parameter Selections

1. 1. What does "Virus" refer to in the selection?

   The "Virus" dropdown allows you to select the type of virus for which data is being retrieved. Options are dynamically loaded based on available virus data in the database.

2. 2. What is a "Surface Protein"?

   "Surface Protein" refers to proteins found on the surface of the selected virus, such as hemagglutinin (HA) or neuraminidase (NA). The options depend on the chosen virus.

3. 3. What does "Subgenera/Subtype" mean?

   "Subgenera/Subtype" refers to a specific subgroup or subtype of the selected protein for the chosen virus, allowing for finer-grained selection.

4. 4. How are "Epitope Size Percentile" values used?

   The "Epitope Size Percentile" values represent the range of accessible surface area (ASA) distribution for epitopes and paratopes in antigen-antibody complexes. The "from" value sets the minimum, and the "to" value sets the maximum percentile.

5. 5. What does "Structural Flexibility Cutoff (RMSD)" stand for?

   "RMSD" stands for Root Mean Square Deviation, which measures the variability in residue positions within a patch. A lower RMSD value indicates less variability.

6. 6. What is the "Subunit Overlap Rate"?

   The "Subunit Overlap Rate" defines the maximum allowable overlap rate for atoms in a patch located at subunit interfaces.

7. 7. What is "Residue Glycan Shielding Rate"?

   This parameter specifies the maximum allowable glycan shielding rate for residues in a patch.

8. 8. What does "Overlap Rate between Patches" mean?

   This parameter sets the maximum allowable atom overlap rate between any two patches.

9. 9. What is the "Atom Overlap Rate in a Patch within 5 Å of Stem Atoms"?

   This parameter defines the maximum allowable atom overlap rate for patches located within 5 Å of stem atoms. This option is specific to certain proteins like NA.