LGA modeler (DIG-SC: deletions, insertions, gaps, side-chains)


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 the protein structure in PDB format for LGA modeling of deletion, insertion and gap automated construction.


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 you will be notified when the results of LGA analysis are completed. Bear in mind that if you enter an incorrect email address there is no way the server can contact you!


Copy and paste the FASTA sequence of your protein structure into the box below:   EXAMPLE


The name of the protein structure that will be analyzed:
  (Optional) name of the protein structure.

There are two ways to enter your protein structure data:

1. Copy and paste your structure data in PDB format into the box below.

or

2. Include the name of your local file containing structure data.
  Protein Structure file
If your PDB structure data is prepared as one file, just select the file containing data and this will be read and uploaded after you click "START".


There are two ways to enter LIST of structures that will be used as templates in DIG processing:

1. Copy and paste your list of PDB chains (max = 100) into the box below:   EXAMPLE

or

2. UPLOAD *.tar.gz file containing set of protein structures for processing (name of your local *.tar.gz file)

NOTE: NO subdirectories within *.tar.gz file!


You can run all calculations automatically, or select one region (with DIG inside)
      DIG auto
      DIG manual. Region:   Beg , End (example of DIG region between 10 and 12; length = 1)

Set chain id for the constructed model: (default: A ; if no chain has to be specified, then type: none)

In order to correlate the residue numbering between the sequence and the structure
the residue number of the first residue in the sequence has to be specified.
Default setting: (the residue number 1 in the sequence corresponds to the residue number 1 in the constructed structure)


When you are ready, click START.


Please send any comments or suggestions concerning
AS2TS - Protein Sequence and Structure services
to Adam Zemla
: adam_zemla@yahoo.com