Max-Planck-Institut für Informatik
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Computational Biology / Bioinformatics II (SS 2008)


Klausureinsicht: Fri Nov 21st, 10-11:30 and 14-15:30, Room 528 MPI
Second Exam results: (pdf)
Second Exam (Nachschreibeklausur): 11th of November, 13:00-16:00, room 023 in the MPI (Building E1 4)
First Exam results: (pdf)


Lecturer: Prof. Dr. Thomas Lengauer, PhD
Tutor: Sven-Eric Schelhorn

Course Details

Language: English
Credit Points: 9 LP (V4 U2)
Module-Identifier: BI-B-3
Modules: "Vorlesungen der Bioinformatik" (Bachelors Program Bioinformatics)

Times and Locations

Lecture: Tuesday and Thursday 14-16h c.t., in Building E1 4 (MPI Building), Room 024
Starting Tuesday, April 15 and ending Thursday, July 10

Tutorials: Wednesday, 14-16h c.t., Building E1 4 (MPI Building), Room 021
Starting Wednesday, April 16 and ending Friday, July 11

Exams: July 15th 1-4 pm in building C4.3 room 0.16. Enter the building by the yard between the physics-tower and the chemistry faculty. Keep to your right in the foyer.


The course concentrates on "downstream" problems in computational biology, i.e. those problems that arise after the basic genome and protein sequence has been analyzed. Problems that are covered include protein structure comparison, protein structure prediction, protein domain and protein family analysis, protein function analysis, analysis of protein interactions (docking), drug comparison and drug screening, analysis of mRNA expression data, analysis of metabolic and regulatory networks, analysis of genetic variations, analysis of resistance patterns in infectious diseases.


The course is obligatory for bioinformatics students and is targeted towards students in the 4th semester. The course is the sequel to the course 'Bioinformatik I'. Students who did not take that course will have to work up on their own some of the basic material on sequence alignment and phylogeny. We strongly suggest that students should also have attended "Mathematik fuer Informatiker I", "Mathematik fuer Informatiker II", and "Programmierung II".

Requirements for the Course Certificate

To obtain the certificates, students have to solve homework assignments and pass the final exam. The final grade is based on the exam alone. Homework assignments will be made available every Thursday on this page. Please return your solutions within one week, the deadline is the following Thursday 14:00h (before the Thursday lecture). All students who achieve at least 50% of possible points in the assignments qualify for the written exam. It is permitted to submit solutions in groups of up to two persons. Remember that you have to register for the final exam according to the regulations that apply to your program of study. Also, do not forget to bring your student's ID card to the exam.

Requirements for the Homework Assignments

The complete solution (incl. source code & command line syntax, if necessary) must be submitted in written form to the postbox in front of room 502 on the 5th floor of Building E1 4 (MPI Building). In addition, for all programming exercises a runnable version of the program must be sent to The subject line of the email must contain the string '[BI2-#]', where '#' should be replaced with the number of the homework assignment. Remember to write your full name in the email body. We strongly encourage that you submit computer printed solutions. In case you plan to hand in hand-written text please observe that we can only grade neat and easily readable sheets. Please read the assignment sheets carefully - there may be deviations from these rules for some assignments as the tutors will change during the course. The solutions to the assignments will be discussed in weekly tutorials. The tutorials will deal with the assignments that have been handed in the week before the tutorial date.

Office Hours

Thomas Lengauer: Thursday, 13:30-14:00h, Building E1 4 (MPI Building), Room 501 and after each lecture in the lecture hall
Sven-Eric Schelhorn: Friday, 16-17h, Building E1 4 (MPI Building), Room 528

Schedule and Downloads

Available: 9 (Bock & Schelhorn) (Optional)
Week Date Lecture Assignment Tutorial
1 Tue, April 15th Lecture 1: Protein Structure (pdf)
Wed, April 16th Tutorial 0 (Schelhorn)
Protein Structure Classification
Thu, April 17th Lecture 2: Protein Structure Comparison (pdf)
Papers: 1 2 3 4 5
Available: 1 (Schelhorn)
Fri, April 18th Tutorial 0b (Schelhorn)
Protein Structure Classification
2 Tue, April 22nd Lecture 3: Introduction to Structure Prediction &
2D Protein Structure Assignment (pdf)
Papers: 1 2
Wed, April 23th (No tutorial)
Thu, April 24th Lecture 4: 2D Protein Structure Assignment &
2D Protein Structure Prediction (pdf)
Changed location: Building E1.4 (MPI) Room 021
Papers: 1 2 3
Due: 1 (Schelhorn)
3 Tue, April 29th Lecture 5: 2D Protein Structure Prediction & Threading (pdf)
Papers: 1 2 3
Available: 2 (Sander)
Example matrix for problem 3
Wed, April 30th Tutorial 1 (Schelhorn)
Discussion of assignment 1
Thu, May 1st (Public holiday)
4 Tue, May 6th Lecture 6: Protein Threading - Protein Disorder (pdf)
Papers: 1 2
Wed, May 7th (No tutorial)
Thu, May 8th Lecture 7: RDP, Protein Disorder (pdf)
Papers: 1 2
Due: 2 (Sander)
Available: 3 (Sommer)
Data for problem 2
5 Tue, May 13th Lecture 8: CASP and de novo Structure Prediction (pdf)
Papers: 1 2
Wed, May 14th Tutorial 2 (Sander)
Discussion of assignment 2
Thu, May 15th Lecture 9: Homology-based modeling (pdf)
Papers: 1 2
Due: 3 (Sommer)
6 Tue, May 20th Lecture 10: Protein Function Prediction and Motif Search in Proteins (pdf)
Book chapter 30 from 'Bioinformatics - from genomes to therapies' (Edited by Thomas Lengauer, Wiley 2007) : pdf
Wed, May 21th Tutorial 3 (Sommer)
Discussion of assignment 3
Thu, May 22th (Public holiday)
7 Tue, May 27th Lecture 11: Genomic Context Methods and Post-translational Modifications (pdf)
Book chapter 31 from 'Bioinformatics - from genomes to therapies' (Edited by Thomas Lengauer, Wiley 2007) : pdf
Available: 4 (Domingues)
Data for problem 1
Pdb-files for problem 3
Pdb-list for problem 3
Wed, May 28th (No tutorial)
Thu, May 29th Lecture 12: Structure-Function Relationships (pdf)
Papers: 1 2
8 Tue, June 3rd Lecture 13: Structure-function relationships, Molecular basis of disease (pdf)
Papers: 1, 2
Wed, June 4th Repetition Tutorial 1 (Schelhorn)
Clique Search, Neural Networks, LP/IP, EMOTIF
Thu, June 5th Lecture 14: Molecular basis of disease, Drug design taxonomy (pdf) Due: 4 (Domingues)
Available: 5 (Kunert)
Wed, June 11th Lecture 15: FlexX (4-6pm!) (pdf) Tutorial 4 (Domingues)
Discussion of assignment 4
Thu, June 12th Lecture 16: FlexX Enhancements and Ligand Superposition (pdf)
Papers: 1, 2, 3, 4
Due: 5 (Kunert)
Available: 6 (Dietzen)
Fri, June 13th Repetition Tutorial 2 (Schelhorn)
TRILOGY, various from lectures 6-8, the Exam
10 Tue, June 17th Lecture 17: FlexX Enhancements (pdf)
Wed, June 18th Tutorial 5 (Kunert)
Discussion of assignment 5
Thu, June 19th Lecture 18: Drug Screening (pdf, ppt)
Papers: 1, 2, 3, 4
11 Tue, June 24th Lecture 19: Statistical issues in HIV resistance (pdf, ppt)
Papers: 1, 2 Movies: 1, 2
Due: 6 (Dietzen)
Available: 7 (Altmann)
Wed, June 25th (No tutorial)
Thu, June 26th Lecture 20: HIV Coreceptor Usage (pdf)
Papers: 1, 2 (required), 3
12 Tue, July 1st Lecture 21: Analysis of ArrayCGH Data (pdf)
Papers: 1, 2, 3
Due: 7 (Altmann)
Available: 8 (Tolosi)
Wed, July 2nd Tutorial 6 (Dietzen)
Discussion of assignment 6
Thu, July 3rd Lecture 22: RNA 2D Structure (pdf)
Papers: 1, 2
Fri, July 4th Repetition Tutorial 2 (Schelhorn)
13 Tue, July 8th Lecture 23: Godot (pdf)
Papers: 1
Due: 8 (Tolosi)
Wed, July 9th Tutorial 7 (Altmann)
Discussion of assignment 7
Thu, July 10th Lecture 24: Analysis of Protein Interaction Networks Due: 9 (Bock)
Fri, July 11th Tutorial 8 (Tolosi)
Discussion of assignment 8
14 Tue, July 15th First Exam
1-4 pm in building C4.3 room 0.16


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