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Chemoinformatics in Drug Discovery - #27618/#27828Course 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.
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 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
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)
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)
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
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
Thursday, October 6, 08:15 - 12:00
Mini-project 1
Thursday, October 13, 08:15 - 12:00
Handing in of reports
Thursday, October 20
(Autumn Holidays)
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
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
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
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
Thursday, November 24, 08:15 - 12:00
Mini-project 2
Thursday, December 1, 09:00 - 12:45
Poster presentations and course evaluation
- 08:30 - 11:15
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Poster presentations (with cookies and refreshments)
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- 11:30 - 12:00
- Course wrap-up and evaluation
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Wednesday, December 14 & Thursday, December 15
Oral Exam
Go to Main Course Page
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