License agreement for the LGA code download

The LGA program is a software developed to facilitate structural comparative analysis of similarities between protein structures.

program by Adam Zemla

Intellectual property rights of designed and developed LGA, GDT, and LCS measures and 
algorithms are protected by US Patent:
Patent No.: US 8,024,127 B2 (45) 

The copyright and other intellectual property rights belong to Adam Zemla (hereinafter 
known as the Author) and the current assignee: DOE, Lawrence Livermore National Security, LLC.

Software License Agreement For Non-Profit Institutions Only

End-users who wish to use the software for commercial purposes should contact Author at: (or

By downloading and using the program you are acknowledging the fact that you agree to 
the terms of the agreement. If do not agree with all terms and conditions of the agreement, 
you may not download, install nor use the program.  

The User of the LGA program (including GDC, GDT, and LCS measures) shall be bound by the following 
terms and conditions:

1) The User will receive the LGA program and any related documentation in confidence and will 
use the program for the purpose of his/her own research.

2) The LGA program should be used at only one location by authorized users. 

3) The User agrees to acknowledge the Author in any publication based in part on results 
produced by the LGA program or any of its developed algorithms and measures (i.e. GDC, GDT, and LCS). 
The publication should include the following primary citation:

   A. Zemla: "LGA - a method for finding 3D similarities in protein structures", Nucleic Acids 
   Research, Vol. 31, No. 13, 2003, pp. 3370-3374.
Additional citations in case of referencing some specifics in GDC, GDT, and LCS measures 
(e.g.: LCS or GDT plots), or selection of point position within residues to represent protein 
backbone for structure superposition calculations (e.g. options: "-atom","-bmo", and "-cb"):

   A. Zemla, C. Venclovas, A. Reinhardt, K. Fidelis, T. J. Hubbard: "Numerical criteria for the 
   evaluation of ab initio predictions of protein structure", PROTEINS: Structure, Function, and 
   Genetics, 1997, Suppl.1, pp. 140-150.

   A. Zemla, C. Venclovas, J. Moult, K. Fidelis: "Processing and analysis of CASP3 protein structure
   predictions", Proteins: Structure, Function, and Genetics, Volume 37, Issue S3, 1999, pp. 22-29.

   A. Zemla, C. Venclovas, J. Moult, K. Fidelis: "Processing and evaluation of predictions in CASP4",
   Proteins: Structure, Function, and Genetics, Volume 45, Issue S5, 2001, pp. 13-21.

   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, 10.1002/prot.22551.
   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.

4) If any modifications to the LGA program or GDC, GDT, or LCS measures are introduced, or any portion of 
the provided LGA software is incorporated into other programs these should be communicated to the Author 
and any publications that result from the modifications should include the appropriate citation to the 
original publication as mentioned in paragraph 3. 

5) The LGA program or any of its components (GDC, GDT, LCS) should not be copied, distributed, transferred 
in any form (internet transfer, discs, hard copies... ) nor sublicensed. The program or its parts 
cannot be sold or incorporated into a commercial software. 

6) The results of research obtained by using the LGA program should not be incorporated into 
any data banks that are subject to license fees or any other payments.

7) The User understands that the LGA program is provided "as is," and no warranty is issued. 
The Author will not be held responsible for any damages caused by the use of the LGA program.

If you wish to obtain the LGA program under the foregoing conditions, please fill in the 
provided form below, and check "I Agree" box which indicates your consent to the terms and 
conditions of the agreement.

An e-mail with a link to download the LGA program will be sent to you after your application 
is reviewed and accepted.

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By clicking the "Submit" button you agree to comply with all the terms and regulations described in the LICENSE AGREEMENT on this page.

If you have any questions or comments regarding this license agreement please sent it
to Adam Zemla at