STRALCP - Structure Alignment-based Clustering of Proteins

A. Zemla, B. Geisbrecht, J. Smith, M. Lam, B. Kirkpatrick, M. Wagner, T. Slezak, C.E. Zhou. "STRALCP structure alignment-based clustering of proteins", Nucleic Acids Research, 2007, Vol. 35, No. 22, Pp. e150; doi: 10.1093/nar/gkm1049 [MEDLINE]

This form allows the submission of the list of protein structures from PDB for STRALCP analysis.

Please 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 STRALCP analysis are completed. Bear in mind that if you enter an incorrect email address there is no way the server can contact you!

  (Optional) name of the experiment.
The name of the experiment (will be used in the subject line in the e-mail to inform you after the calculations are completed):

Parameters for STRALCP calculations:

Additional LGA parameters (experts only):
  LGA parameters

COPY AND PASTE your PDB list of models (chains, domains) into the box below (no more than 25 PDB entries; one chain specification per line):   EXAMPLES

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'
   1akf       for PDB entry: 1akf, chain: ' '
or specifying NMR MODEL:
   1bve_B_5   for PDB entry: 1bve, chain: 'B', model: 5 
   1rel___4   for PDB entry: 1rel, chain: ' ', model: 4

It is recommended that the structures are split into separate domains.   
For details how to specify ranges in calculated structures please check EXAMPLE and LGA parameters.

OR 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!

Examples of STRALCP calculations on selected Folds from SCOP: STRALCP_SCOP

Please send any comments or suggestions concerning
AS2TS - Protein Sequence and Structure services
to Adam Zemla