LigCSRre: Ligand similarity search.


  1. LigCSRre is intended for searching banks for compounds similar to a query, based on both coordinates and physico-chemical properties of atoms.
  2. LigCSRre is based on a geometric tool, the CSR algorithm developped by M. Petitjean, that aims at identifying the maximal common substructure in two collections of coordinates, independently of any a priori pairings. It is combined with a regular expression mechanism applied to the mol2 atomic types to increase the physico-chemical relevance of the matches.
  3. LigCSRre is a tool that results from a collaborative work involving several teams at RPBS.
  4. wwLigCSRre is an online server for small applications, available at: Mobyle@RPBS



PLEASE READ THE FOLLOWING LICENSE AGREEMENT. BY USING THE PROGRAM YOU ARE
ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS
AGREEMENT.
USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES
NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: pierre.tuffery  _at_  univ-paris-diderot.fr


 LigCSRre (C) 2008, 2009 - Small compounds 3D molecular similarity screening by:

Pierre Tuffery(1), Flavien Quintus(1), J. Grynberg(1), O. Sperandio(1), M. Petitjean(2)
                        (1): MTi, INSERM UMR-S 973, Université Paris Diderot - Paris 7, F75013, Paris, France.
                             (http://www.mti.univ-paris-diderot.fr)
                        (2): CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), F91191, Gif-sur-Yvette, France.

 

                          GENERAL LICENSE &  CONFIDENTIALITY AGREEMENT

In regard to the small compounds 3D molecular similarity screening program (LigCSRre) herewith (the Software) the copyright and other intellectual property rights to which belong to the Author(s).

Any user (the User) of the program undertakes to the Copyright holder that he or she shall be bound by the following terms and conditions:-

1. The User will receive the Software and any related documentation in confidence and will not use the same except for the purpose of their own
research. The Software will be used only by such of the User's officers or employees to whom it must reasonably be communicated to enable them to
undertake their research and who agree to be bound by the same confidence.
The User shall procure and enforce such agreement from his or her staff for the benefit of the Copyright holder.

2. The publication of research using the Software must include an appropriate citation to the method:

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity,  F. Quintus, O. Sperandio, J. Grynberg, M. Petitjean and P.Tuffery, BMC bioinformatics, in press.

3. All forms of the Software will be kept in a reasonably secure place to prevent unauthorised access.

4. Each copy of the Software or, if not practicable then, any package associated therewith shall be suitably marked (and such marking maintained)
with the following copyright notice: "Copyright 2008 Pierre Tuffery, Flavien Quintus, J. Grynberg, O. Sperandio, M. Petitjean, All Rights Reserved.".

5. The Software may be modified, but any changes made shall be communicated to the Author(s) and made freely available. Any modified version of The Software
will remain subject to the terms of this license.

6. The Software may not be sold as a standalone package, or incorporated into a commercial software package without the written permission of the Copyright
holder. The Software may be used freely for individual academic or non-commercial research. The Software is also freely available for training or
teaching purposes.

7. The results produced by the Software may not be incorporated into any data banks or databases which are subject to the payment of access or
license fees without the written permission of the Copyright holder.

8. The Software may be made available to users over a local network or wide area network (including the Internet), but only if access is granted
free of charge to all authorised users. Incorporation of the Software into a commercial Web site or other fee paying service is not allowed without
the written permission of the Copyright holder. If LigCSRre results are returned to the user via such a network service, then a suitable
acknowledgement of the LigCSRre method must be returned somewhere in the output text.

9. The confidentiality obligation in paragraph one shall not apply:

   (i)  to information and data known to the User at the time of receipt hereunder (as evidenced by its written records);

  (ii)  to information and data which was at the time of receipt in the public domain or thereafter becomes so through no wrongful act of
        the User;

 (iii)  to information and data which the User receives from a third party not in breach of any obligation of confidentiality owed to
        the Author(s).

10. The User understands that the Software is supplied "as is". No warranty as to its fitness or suitability for any purpose whatsoever is made or implied. In no event shall the Author(s) or Copyright holder be held
   responsible for any direct or indirect damages arising through the use of the Software.