Citing LGA:
Zemla A., "LGA - a Method for Finding 3D Similarities in Protein Structures", Nucleic Acids Research, 2003, Vol. 31, No. 13, pp. 3370-3374. [MEDLINE]

This form allows the submission of two 3D protein structures (coordinates in PDB format) for LGA pairwise processing.

LGA program is being developed for structure comparative analysis of two selected 3D protein structures or fragments of 3D protein structures (see: HELP for more information). As a result of LGA processing user will get the rotated coordinates of the first structure, and (optionally) the coordinates of the second structure (target, not changed).

NOTE: If you need to compare one structure with a set of structures from a given list, then we recommend using our LGA - PDB chains structure comparison service. Using this service you can select one structure as a frame of reference (target) and compare it with all other structures from your list.

First enter your email address in the box below.
E-mail
Be sure that your email address is correct.
Your data will be processed and the result of LGA analysis sent automatically to the above address. Bear in mind that if you enter an incorrect email address there is no way the server can contact you!

There is the default set of parameters in the box below. Depending on your needs you can change these parameters.
LGA parameters

You have four different ways to enter your structure data:

Use PDB code of the structures to be analyzed.

1. Include two PDB codes of the chains of proteins you would like to process.
Coordinates of the second molecule will not be changed.
For example:   1sip_A   1cpi_B

In this example the PDB entry 1sip chain A (use _A to indicate chain A) is selected
as a first molecule, and 1cpi protein chain B is included as a second molecule.

Please make sure that you select PDB chains (and domain ranges) correctly. Otherwise NO RESULTS will be calculated.

PDB_entry has to be in the following format:
   1cpi_A     for PDB entry: 1cpi, chain: 'A'
   1afk       for PDB entry: 1afk, chain: ' '
   1ggg*      for PDB entry: 1ggg, all existing chains are selected (chain 'A' and 'B')
or specifying NMR MODEL:
   1bve_B_5   for PDB entry: 1bve, chain: 'B', model: 5
   1rel___4   for PDB entry: 1rel, chain: ' ', model: 4

For details how to specify ranges in claculated structures please check LGA parameters.

An alternative is to use the 'File Upload' option. Just select two files containing your 3D protein structures in the format of the PDB standard ATOM records and these will be read and sent after you click "START".

2. Include the names of your local files containing structures data.
    (to rotate)
    (no change)

If your data is prepared as one file, just select the file containing your two-structures data and this will be read and sent after you click "START".

3. Include the name of your local file containing two-structures data. Each one of the two 3D structures should begin with MOLECULE and end with END record (see: format description):
  Two molecules in one file

Another alternative is to enter structures (copy and paste your data) into the window below.

4. Paste your data into the box below. Each one of the two 3D structures should begin with MOLECULE and end with END record (see: format description):

If you are using option 1, 2 or 3 you can select:
      Run LGA now
      Upload selected file
Then click START.