Molecular visualization in the rational drug design process
Matthias Keil1, Richard J. Marhofer2, Andreas Rohwer2, Paul M. Selzer2, Jurgen Brickmann3 Oliver Korb4, Thomas E. Exner4
1
Tripos International, 1699 South Hanley Road, St. Louis, MO 63144-2319, USA, current address: Chemical Computing Group Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Quebec, H3A 2R7, Canada, 2Intervet Innovation GmbH, BioChemInfomatics, Zur Propstei, 55270 Schwabenheim, Germany, 3Department of Chemistry, Darmstadt University of Technology and MOLCAD GmbH, Petersenstr. 20, 64287 Darmstadt, Germany, 4Fachbereich Chemie, Universitat Konstanz, 78457 Konstanz, Germany
TABLE OF CONTENTS
- 1. Abstract
- 2. Overview of the drug design process
- 2.1. Textbox 1
- 2.2. Standard representations
- 3. Protein structure prediction
- 3.1. Textbox 2
- 3.2. Simplified molecular representations and special features
- 4. Binding-site identification and characterization
- 4.1. Textbox 3
- 4.2. Molecular surfaces and mapped properties
- 5. Protein-ligand docking
- 5.1. Textbox 4
- 5.2. Three-dimensional data fields
- 6. Ligand-based design
- 6.1. Textbox 5
- 6.2. Three-dimensional vector fields
- 7. Ligand optimization
- 7.1. Textbox 6
- 7.2. Interactive modeling
- 8. Conclusion
- 9. Acknowledgement
- 10. References
1. ABSTRACT
The visualization of molecular scenarios on an atomic level can help to interpret experimental and theoretical findings. This is demonstrated in this review article with the specific field of drug design. State-of-the-art visualization techniques are described and applied to the different stages of the rational design process. Numerous examples from the literature, in which visualization was used as a major tool in the data analysis and interpretation, are provided to show that images are not only useful for
