Erice2008:workshop4
From DISI
This is the detailed information for workshop #4, CCDC Tools.
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Aim
Whether you are a crystallographer trying to generate the best possible model that fits the diffraction data, or a molecular modeller starting a program of work to discover novel active leads, understanding what your protein/ligand structural model is telling you is crucial. This workshop will show you how to:
• compare a structure with closely homologous structures
• identify which parts of the protein/ligand interface may have errors
• identify which waters are conserved and which might be easily displaced
• establish whether a particular conformation is unusual
• characterise interactions between the ligand and the protein
In particular we will explore the use of small molecule inter- and intra-molecular geometric information to evaluate the quality of a protein/ligand structural model and to identify cases where binding to the protein leads to significant strain within the ligand.
These investigations will be carried out using the Relibase+ program and the Cambridge Structural Database system (CSDS).
Suitability
The workshop will be presented in a “watch the expert” format in one session and as a “hands on” format in another session. Both will be suitable for the complete novice. However we will also cater for the more advanced user in the “hands on” session.
Materials
Useful background reading before the workshop:
• Relibase - Design and Development of a Database for Comprehensive Analysis of Protein-Ligand Interactions M. Hendlich, A. Bergner, J. Günther, G. Klebe, J. Mol. Biol., 326, 607-620, 2003.
• Utilising Structural Knowledge in Drug Design Strategies: Applications Using Relibase J. Günther, A. Bergner, M. Hendlich and G. Klebe, J. Mol. Biol., 326, 621-636, 2003
• Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis, K.A. Brameld, B. Kuhn, D.C.Reuter and M. Stahl, J. Chem. Inf. Model, 48, 1-24, 2008
• Life-science applications of the Cambridge Structural Database, R. Taylor, Acta Cryst. D, 58, 879-888, 2002
websites to review before the workshop
Protocol
How to access the Workshop:
Use a browser to access: http://relibase.ccdc.cam.ac.uk
Use the following email address to access the workshop workspace: demo@ccdc.cam.ac.uk
Use the password s1mple
Follow the handout below and enjoy !
Building Solid Foundations for a Structure Based Design Campaign – Workshop handout Erice 2008
Extras
Here are the "bonus projects" you may work on if you finish the workshop early.
- 1.
