Computer-Aided Drug Design Teaching
Web site for the Computer-Aided Drug Design lecture and practices provided by the Computer-Aided Molecular Engineering Group of the University of Lausanne and the Molecular Modelling Group of the SIB Swiss Institute of Bioinformatics.
To follow the exercises, please, install the "current production release" version of UCSF Chimera by following this link: Download UCSF Chimera and AutoDock VINA 1.1.2 by following this link: Download AutoDock VINA.
To follow the exercises, please, install the "current production release" version of UCSF Chimera by following this link: Download UCSF Chimera and AutoDock VINA 1.1.2 by following this link: Download AutoDock VINA.
Lecture
The PDF file of the lecture's slides can be found for Session 1, Session 2, Session 3 and 4, Session 5 and Session 6 -->and Session 7.
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Prologue: molecular representations
Introduction to (computer-aided) drug design
Origin of 3D structures
Molecular recognition
Binding free energy estimation
Introduction to molecular docking
Introduction to molecular (virtual) screening
Short introduction on target prediction of small molecules
Introduction to ADME, pharmacokinetics, druglikeness
Short introduction to bioisosterism
Practice
The PDF file of the practice booklet can be found here.
Practice session 1: Introduction to UCSF Chimera
Exercise 1. UCSF Chimera hands on - Loading a structure, moving, zooming, selecting, rendering, analyzing and savingExercise 2. Using surfaces in UCSF Chimera
Exercise 3. Using lightnening and effects in UCSF Chimera
Exercise 4. Loading several structures and aligning with the MultiAlign Viewer
Practice session 2. Ligand-protein docking
Exercise 5. Docking of anti-inflammatory drug Celecoxib into protein COX2Exercise 6. Structure-based optimization of COX2 inhibitors