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Shop

Shop is extremely useful to guide the Scaffold Hopping procedure during the Drug Discovery process [ J. Chem. Inf. Comput. Sci. 45, 1313-1323 (2005)].

Scaffold Hopping is the methodology that substitutes one part of a molecule with another one, retaining their pharmacophoric interaction points. Shop is doing much more. In a fully integrated approach, it maintains 3D interaction capabilities and considers, at the same time, the synthetic feasibility and the ADME profiles of the potential candidates.

The method proposed in Shop is simple and ready to use and based on a client/server application. The User can generate scaffold databases that are searchable using geometric constraints, interaction pattern based on GRID force field and shape criteria. The results are directly aligned on top of the query scaffold for an easy understanding and evaluation of the new chemicals.

A sample database has been built* based on the scaffolds used in combinatorial chemistry and collected in the comprehensive surveys of combinatorial library synthesis (see references below). The user can download this database from Lead Molecular Design and decompress it on the ShopDir/databases folder. Then re-start the server and when the user is connected from the client this database will be available.


REFERENCES

  1. SHOP: a method for structure-based fragment and scaffold hopping.
    Fontaine F, Cross S, Plasencia G, Pastor M, Zamora I.
    ChemMedChem, 2009, 4 (3), pp 427–439
  2. SHOP: Receptor-Based Scaffold HOPping by GRID-Based Similarity Searches.
    Rikke Bergmann, Tommy Liljefors, Morten D. Sørensen and Ismael Zamora
    J. Chem. Inf. Model., 2009, 49 (3), pp 658–669
  3. SHOP: Scaffold HOPping by GRID-Based Similarity Searches.
    Bergmann R, Linusson A, Zamora I.
    J. Med Chem.,2007, 50 (11), pp 2708–2717 (2007)
  4. Marie M. Ahlström, Marianne Ridderström, Kristina Luthman, and Ismael Zamora
    Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields
    J. Chem. Inf. Model., 2005, 45 (5), pp 1313–1323
  5. Comprehensive survey of combinatorial library synthesis: 2004
    Roland E. Dolle
    J. Comb. Chem. 7, 739-798 (2005)
  6. Comprehensive survey of combinatorial library synthesis: 2003
    Roland E. Dolle
    J. Comb. Chem. 6, 623-679 (2004)
  7. Comprehensive survey of combinatorial library synthesis: 2002
    Roland E. Dolle
    J. Comb. Chem. 5, 693-753 (2003)
  8. Comprehensive survey of combinatorial library synthesis: 2001
    Roland E. Dolle
    J. Comb. Chem. 4, 369-418 (2002)
  9. Comprehensive survey of combinatorial library synthesis: 2000
    Roland E. Dolle
    J. Comb. Chem. 3, 477-517 (2001)
  10. Comprehensive survey of combinatorial library synthesis: 1999
    Roland E. Dolle
    J. Comb. Chem. 2, 383-433 (2000)

* TERMS AND CONDITIONS FOR THE USE OF COMBCHEM SHOP DATABASE
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PLEASE READ THIS CAREFULLY.
By using the CombChem database you are agreeing to accept these terms and
conditions. Every user may only use it as described in the Regular MD
Licence Terms (or other written agreement with MD) on an authorised date,
at an authorised site. Networking to or from other sites is not permitted.
MD gives no warranties that this databases are suitable for any particular
purpose. MD accepts no responsibility for any mathematical or scientific
or technical errors or limitations of this database.
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