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Chemoinformatics in Drug Discovery - #27618/#27828

Course Programme, Autumn 2011

In the autumn semester, CBS is offering a MSc/PhD course in Chemoinformatics in Drug Discovery. The course starts on September 1 and runs every Thursday morning from 8 to 12.

Lectures and exercises take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 210, auditorium 52, in Lyngby.

Course Organizers: Olivier Taboureau   and   Irene Kouskoumvekaki

Please note: The content of powerpoint slides and handouts is based on last year's course and may thus change slightly the week before each lecture.




O Thursday, September 1, 09:00 - 12:00

Introduction

09:00 - 09:30
Introduction to the course
Slides: (Introduction to course)

09:30 - 10:00
Introduction to UNIX
Slides: (Introduction to UNIX)

10:15 - 12:00
Introduction to Chemoinformatics
Slides: (Introduction to Chemoinformatics)

Reading Material: Chemoinformatics, Chapters 1 & 10.4 (10.4.1-10.4.6), Review article



O Thursday, September 8, 08:15 - 12:00

Small molecule databases

08:15 - 09:00
Representation of molecular structures and structural similarity
Slides: (Lecture slides)

09:15 - 10:00
Chemical databases and database searching
Slides: (Lecture slides)

10:15 - 12:00
Exercise (Exercise)

Reading Material: Chemoinformatics, Chapter 2 (2.1-2.4, 2.7.1, 2.8.1-2.8.2, 2.8.6, 2.9.1-2.9.4, 2.11.2, 2.12), Chapter 5 (5.1-5.3) and Chapter 6 (6.1-6.2, 6.4.1-6.4.2)



O Thursday, September 15, 08:15 - 12:00

Molecular descriptors

08:40 - 09:10
Molecular descriptors -1
Slides: (Lecture slides)

09:20 - 10:00
Molecular descriptors -2
Slides: (Lecture slides)

10:15 - 12:00
Exercise
Slides: (Exercise)

Reading Material: Chemoinformatics, Chapter 8 (8.1-8.4, 8.7-8.8)



O Thursday, September 22, 08:15 - 12:00

Clustering methods and simple regression methods

08:15 - 09:00
Linear methods for visualization and regression
Slides: (Lecture slides)

09:15 - 10:00
Clustering with Self-Organizing Maps
Slides: (Lecture slides)

10:15 - 12:00
Exercise
Exercise   Article-SOM

Reading Material: Chemoinformatics, Chapter 9 (9.1-9.2, 9.4, 9.5.1, 9.5.3-9.5.4) and Chapter 10 (10.1.3, 10.4.7.1)

Software: MDM by molegro




O Thursday, September 29, 08:15 - 12:00

Non-linear classification and regression methods

08:15 - 09:00
Decision Trees and Artificial Neural Networks
Slides: (Lecture slides)

09:15 - 10:00
Genetic Algorithms and Support Vector Machines
Slides: (Lecture slides)

10:15 - 12:00
Exercise (Exercise)

Reading Material: Chemoinformatics, Chapter 4 (4.1-4.2, 4.3.1, 4.3.3, 4.4), Chapter 9 (9.3, 9.5.2, 9.5.5-9.5.9, 9.7-9.8) and Article_SVM  



O Thursday, October 6, 08:15 - 12:00

Mini-project 1




O Thursday, October 13, 08:15 - 12:00

Handing in of reports



O Thursday, October 20

(Autumn Holidays)



O Thursday, October 27, 08:15 - 12:00

Virtual screening methods: pharmacophore, docking

08:15 - 09:00
Virtual screening - pharmacophore
Slides: (Lecture slides)

09:15 - 10:00
Docking
Slides: (Lecture slides)

10:15 - 10:45
Feedback on mini-project 1
Slides:

10:45 - 12:00
Exercise
Exercise: (Exercise)

Reading Material: Article_1,   Article_2

Software: MOE by Chemical Computing Group



O Thursday, November 3, 08:15 - 12:00

Property prediction: a) ADMET properties and bioavailability of drugs, b) Physicochemical properties of drugs

08:15 - 09:00
ADME
Slides: (Lecture slides)

09:15 - 10:00
Toxicity
Slides: (Lecture slides)

Exercise
Exercise - Docking: (Exercise)

Reading Material: Chemoinformatics, Chapter 10 (10.1.5-10.1.7) and Article

Software: MOE by Chemical Computing Group, MDM by molegro



O Thursday, November 10, 08:15 - 12:00

Pharmacological profiling of chemical compounds

08:15 - 09:00
Chemical-protein interaction networks and visualization tools
Slides: (Lecture slides)

09:15 - 09:45
Systems Pharmacology
Slides: (Lecture slides)

Mini-project 2

Reading Material: Article_1,   Article_2



O Thursday, November 17, 08:15 - 12:00

Systems Chemical Biology

08:15 - 09:00
Text mining for drugs and chemical compounds
Slides: (Lecture slides)

09:15 - 09:45
Case Study: Drug target identification using side effect similarity
Slides: (Lecture slides)

Mini-project 2

Reading Material: Article_STITCH,   Article_side-effects  




0 Thursday, November 24, 08:15 - 12:00

Mini-project 2



O Thursday, December 1, 09:00 - 12:45

Poster presentations and course evaluation

08:30 - 11:15
Poster presentations (with cookies and refreshments)

11:30 - 12:00
Course wrap-up and evaluation


O Wednesday, December 14 & Thursday, December 15

Oral Exam



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