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{{Infobox script-repo
|type      = plugin
|filename  = plugins/lisica.py
|author    = Janez Konc
|license   = 
}}

== Description ==

LiSiCA is a software for 2D and 3D ligand based virtual screening. It uses a fast maximum clique algorithm to find two- and three- dimensional similarities between reference compound and a database of target compounds in Mol2 format. The similarities are expressed using Tanimoto coefficients and the target compounds are ranked accordingly.

Plugin is developed and maintained by National Institute of Chemistry, Slovenia. 


== Requirements ==

The plugin should work on Winodws and all variety of Unix like systems. Most of the tests were performed on Windows 7, Ubuntu 14.04 and Linux Mint.  
To work properly, the plugin requires Python with Tkinter and PyMOL. The plugin was maily tested with PyMOL 1.7.

== Installation == 

This plugin is ready "out-of-box" for both Linux and Windows users through the project Pymol-script-repo. 

The lisica.py script initializes the installation of the plugin.
It performs the following functionalities:
1. Downloads and installs all the required files (python modules, icons, executables).
2. Prompts user for Activation code on installation. (See section: Licensing)
3. Once the files are properly installed and the license activated, LiSiCA plugin version will be ready to use.


'''Important note''': For complete installation of the plugin, a stable internet connection is required at the user end.  

==Plugin Features == 

1. Graphical User Interface which facilitate the choice of parameters for LiSiCA.
2. Results displayed according to the ranking in similarities as measured by Tanimoto coefficients.
3. Similarity between molecules visualized on PyMOL viewer.







==  Reference == 


'''If you are using LiSiCA in your work, please cite:'''

S. Lesnik, T. Stular, B. Brus, D. Knez, S. Gobec, D. Janezic, J. Konc, LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors, J. Chem. Inf. Model., 2015, 55, 1521–1528.

[http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00136 Read the article] 

[http://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5b00136 PDF Link]




==  Licensing == 

LiSiCA software is copyrighted by : 

Janez Konc
National Institute of Chemistry
Laboratory for Molecular Modeling
Hajdrihova 19
SI-1000 Ljubljana
Slovenia.

For using LiSiCA plugin, an Activation Key is  required. To obtain the key, email to [email protected] providing your title, full name, institutuion, laboratory, supervisor name. Also, kindly state your intended usage of the software.

This software is copyrighted by Janez Konc ([email protected]).
The following terms apply to all files associated with the software 
unless explicitly disclaimed in individual files.
 
    '''LiSiCA SOFTWARE LICENSE AGREEMENT'''
 
  1. Grant Of Limited License; Software Use Restrictions. The programs received by you will be used only for NON COMMERCIAL purposes.
     This license is issued to you as an individual.
     
     For COMMERCIAL use of the software, please contact Janez Konc for details about commercial usage license agreements.
     For any question regarding license agreements, please contact:
     
     Janez Konc
     National Institute of Chemistry
     Laboratory for Molecular Modeling
     Hajdrihova 19
     SI-1000 Ljubljana
     Slovenia.
     
  2. COMMERCIAL USAGE is defined as revenues generating activities. These
     include using this software for consulting activities and selling
     applications built on top of, or using this software. Scientific 
     research in an academic environment and teaching are considered 
     NON COMMERCIAL.
 
  3. Copying Restrictions. You will not sell or otherwise distribute commercially 
     these programs or derivatives to any other party, whether with or without 
     consideration.
 
  4. Ownership of Software. You will not obtain, and will not attempt to 
     obtain copyright coverage thereon without the express purpose written 
     consent of Janez Konc.
 
  5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY
     FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
     ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY
     DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE
     POSSIBILITY OF SUCH DAMAGE.
 
  6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES,
     INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
     FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT.  THIS SOFTWARE
     IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
     NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
     MODIFICATIONS.