Citing LGA program, GDT and LCS measures:
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. The two novel measures LCS and GDT have been designed and developed by Adam Zemla to serve as a basis for a scoring function of the LGA alignment algorithm. 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).

Structure comparative analysis can be made in two general modes:

• (Experts only) Superpositions are calculated using "fixed residue-residue correspondence" (options: -1, -2, -3).
  This mode can be used when user knows how to establish residue-residue correspondence for LGA processing (see options: -ch1, -aa1, -gap1, -er1, -sda, -al). With this mode the residue-residue correspondence will not be changed during the calculations. For example by using the option "-3 -sda" the program will select for calculations the residues that are identical ("-sda") by the numbering of amino acid and chain id, and then identify the fragments where two structures are similar or structurally different ("-3": LCS and GDT analysis).

• (Default) Automated search for residue-residue correspondence and "best" superposition (option: -4).
  This mode can be used for structural comparison of any two proteins. For example using the option "-4 -sia" the best superposition (according to the LGA technique) is calculated completely ignoring sequence relationship ("-sia") between the two proteins, and the suitable amino acid correspondence (structural alignment) is reported ("-4": LGA analysis).

NOTE: A set of additional new GDT-like measures GDC (Global Distance Calculation) allows detailed structure comparison and evaluation of structure similarity of proteins using all atoms or a list of selected atom positions (see: HELP for more information).
D. A. Keedy, C. J. Williams, J. J. Headd, W. B. Arendall III, V. B. Chen, G. J. Kapral, R. A. Gillespie, J. N. Block, A. Zemla, D. C. Richardson, J. S. Richardson. "The other 90% of the protein: Assessment beyond the Calphas for CASP8 template-based and high-accuracy models", Proteins: Structure, Function, Bioinformatics, 2009, 77, pp. 29-49. [MEDLINE]

By default the calculations are performed on CA atoms. However, user can select other than CA atoms or define position within residues on which the calculations will be made (see: LGA parameters for more information, e.g. options: "-atom","-bmo", and "-cb").

First enter your email address in the box below.
  (Optional) 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 a default set of parameters in the box below.
Depending on your needs you can change these parameters.
see: LGA parameters
For tighter superposition "-d:4.0" option is recommended (default: "-d:5.0").
For details of how to select parameters or ranges in the submitted structures, please see HELP.

Now, you have four different ways to enter your structure data for processing:

Use PDB code of the structures to be analyzed.

1. Include two PDB codes of protein structures you would like to process (chains have to be identified).
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 codes correctly. Otherwise NO RESULTS will be calculated.

Examples of the format to specify PDB_chains:
   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')
NMR models can be specified as follows:
   1bve_B_5   for PDB entry: 1bve, chain: 'B', model: 5
   1rel___4   for PDB entry: 1rel, chain: ' ', model: 4

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. Upload your local files containing structure data or name the PDB codes:
Molecule1 to rotate   local:   or   PDB code:  
Molecule2 no change   local:   or   PDB code:  

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