This form allows the submission of the protein structure (target, reference structure) in PDB format for STRALSV analysis. Target structure will be structurally compared with all proteins from the provided list of PDB chains. Structural target will be split into smaller Structure Context fragments, and each fragment will be evaluated separately. Results from all identified structure similarity regions will be combined and observed amino acid variabilities will be reported.

Citing STRALSV:
Zemla A.T, Lang D.M, Kostova T, Andino R, Zhou C.L. "StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.", BMC Bioinformatics. 2011 Jun 2;12(1):226. [MEDLINE]

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

Job name (e.g. the name of the target protein structure):
  (Optional) name of the job.

Parameters for STRALSV calculations:

Length of the Structure Context Sliding Window:
  (minimum length: 20)

LGA distance cutoff (tightness of calculated superpositions):
  AUTO   or   f.f   (fixed: 0.5 <= f.f <= 6.0)

There are three different ways to enter your protein structure (target, reference structure) data:

1. Copy and paste coordinates of your reference structure (PDB format: ATOM records) into the box below.

or

2. Print your PDB code (PDB entry) into the box below (use chain specification if exists, for example: 1cpi_A).
  Name of the PDB chain.

or

3. 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" below.

There are three ways to enter list of PDB structures that will be compared with the selected target structure:

1. Copy and paste your list of PDB chains into the box below (no more than 200 PDB entries; one chain specification per line):   EXAMPLES

or

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

or

3. 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!

RUN calculations