A100 - Activation Index

Calculates the Universal Activation Index for Class A GPCRs (A100).

Instructions:

Please select a .pdb/.ent/.cif structure file or specify a RCSB PDB ID
(optional) Please specify a chain name of the structure that contains the GPCR (default: A)
(optional) Please specify a range of non-GPCR (e.g. T4L, nanobody) residue numbers within the specified chain that should be deleted and thus be excluded from the alignment.

Please use this format: {lowest residue number to be excluded}-{highest residue number to be excluded}
By default, the residue number range “1000-2000” is excluded. If this does not apply to the specified chain of the structure, please specify a different range.
If no residues should be excluded (i.e., all residues of the specified chain should be considered for the alignment), please specify “0-0”.

Start the calculation by submitting the form below.
Check if errors/ warnings occurred and change the parameters accordingly.

In some cases, the alignment might not find the correct most conserved residue numbers in one or even more of the seven transmembrane domains (output by warnings/errors). In such cases, please look for the respective most conserved residue numbers (Ballesteros numbers 1.50 - 7.50) elsewhere (e.g. GPCRdb (https://www.gpcrdb.org/) and specify these residue numbers with the respective -TM(1-7)_50 options.

Required settings

Upload/define structure:

(*.pdf, *.cif (PDBx/mmCIF), *.ent)
OR

RCSB PDB ID (file will be downloaded):

Optional settings:

(-chain) Chain name of structure that contains the GPCR (default: A):

(-del_res) Exclude the specified non-GPCR (e.g. T4L, nanobody) residue number range of the selected chain from the alignment (default: 1000-2000, disable with: 0-0):

(-TM1_50) Residue number of the most conserved amino acid in TM1 (1.50):

(-TM2_50) Residue number of the most conserved amino acid in TM2 (2.50):

(-TM3_50) Residue number of the most conserved amino acid in TM3 (3.50):

(-TM4_50) Residue number of the most conserved amino acid in TM4 (4.50):

(-TM5_50) Residue number of the most conserved amino acid in TM6 (5.50):

(-TM6_50) Residue number of the most conserved amino acid in TM6 (6.50):

(-TM7_50) Residue number of the most conserved amino acid in TM7 (7.50):

Download the script:

Command line script and instructions: Universal_Activation_Index_100_Script.zip.