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.

Lecture
The PDF file of the lecture's slides can be found for Session 1, Session 2, Session 3 and 4, Session 5, Session 6

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

Introduction to quantum methods for drug design

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 saving

Exercise 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 COX2

Exercise 6. Structure-based optimization of COX2 inhibitors

Practice Session 3. Ligand-based virtual screening with SwissSimilarity

Exercise 7. Enrichment of anti-fungal molecules in FDA-approved drugs

Practice Session 4. Reverse screening with SwissTargetPrediction

Practice Session 5. Pharmacokinetics evaluation with SwissADME

Exercise 8. Pharmacokinetics optimization of EGFR inhibitor

Practice Session 6. Bioisosteric design with SwissBioisostere

Practice Session 7. Use of WebMO to perform quantum chemical calculations