LGA pdblist
Structure comparison of models from selected PDB list

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]

Citing GDC (Global Distance Calculation):
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]

Citing LGA when other than CA atoms are used for superposition calculations (options: "-atom","-bmo", and "-cb"):
A. Zemla, C. Ecale Zhou: "Structural re-alignment in an immunogenic surface region of ricin A chain", Bioinformatics and Biology Insights, 2008, v. 2, pp. 5-13. [PMCID]

This form allows the submission of the protein structure (TARGET - reference structure) in PDB format for LGA comparison with structures from the selected LIST of pdb chains. All listed pdb chains will be compared to the TARGET structure.

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

Parameters for LGA calculations:

Distance coloring scheme parameter (deviations below the cutoff are colored in green):
  Range: 0.1 - 10.0

Distances presented on the plot:
Standard (CA)    Max    CB Atoms    Sidechain Atoms (GDC_sc)    CB-CA

Sorting parameter:
Name    N    RMSD    Seq_ID    LGA_S

Job name (e.g. the name of the TARGET structure that will be compared with all structures provided in the LIST section below):

There are three different ways to enter your protein structure (TARGET - reference structure) data:

1. Copy and paste your TARGET structure in PDB format (ATOM coordinates) into the box below.


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


3. Include the name of your local file containing TARGET structure.
  TARGET structure file
If your TARGET structure 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 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 entries; one chain specification per line):   EXAMPLES


2. Include the name of the local file containing your LIST of pdb chains
  local 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.


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

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