DM840 - Algorithms in Cheminformatics

Algorithms in Cheminformatics

DM840, Fall 2014

Daniel Merkle


21.01.2015: Exam Information online (including final question list).

04.01.2015: Exam Information online.

20.10.2014: The second mandatory assignment including both options is online.

29.09.2014: New articles and Weekly Notes online.

16.09.2012: The first mandatory assignment is online.

08.09.2014: Weekly notes for 36 and week 37 and reading material is online.

29.08.2014: Site Launch.


Weekly Notes

The slides material presented in the lectures can be found in the Blackboard System.

DateTopicWeekly Notes
Week 36 Introduction, Course overview, Polya enumeration (teaser), Double Pushout Approach Week 36
Week 37 Double Pushout Approach, Graph Grammars, Exploring Chemical Spaces via Graph Grammars, Subgraph Isomorphism (Ullmann algorithm), Introduction to the first mandatory project Week 37
Week 38 More on graph isomorphism, McKay's Canonical Graph Labeling Algorithm, Introduction to the first Mandatory Assignment, Week 38
Week 40 Even more on graph isomorphism (traces), Ring Perception Week 40
Week 41 Even more on Ring Perception, MCB, Horton's algorithm, de Pina's algorithm, Introduction to the 2nd mandatory project Week 40
Week 43 Petri Nets (in Chemistry and Systems Biology) t.b.a.
Week 44 More on Petri Nets, NPc proof for a reachability problem, more on Graph Isomorphism
Week 46 Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA
Week 47 more on Quantitative structure-activity relationship QSAR, Molecular Descriptors, Principal Component Analysis PCA, why not to use SMILES
Week 48 Mathematical Concepts in Systems Biology, Stoichiometric Models, Flux Balance Analysis, Extreme Pathways
Week 49 Analytic Combinatorics, Generative Functions
Week 50 Polya Counting, Counting in Chemistry, Exercises Exercises
Week 51 Process Algebras Exercises

Office Hours

Just write a short mail, and come by.

  • Office: IMADA, 14-602b-2 map.
  • Phone: 2322
  • E-mail: daniel


In addition to the books we will use original articles as a source of information.

Course Description

The official course description can be found here.

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