The LGA program is a software developed to facilitate structural comparative analysis of similarities between protein structures.
LOCAL-GLOBAL ALIGNMENT FOR FINDING 3D SIMLARITIES IN PROTEIN STRUCTURES (LGA)
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:
firstname.lastname@example.org (or email@example.com).
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 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 implemented algorithms or measures (e.g. LCS, GDT, GDC).
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 LCS, GDT, and GDC 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 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 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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