Friday, March 11, 2011

Pharmaceutical Bioinformatics

The Wikberg group at Uppsala University where I did my first two years of post-docing in Sweden has a (free) course on pharmaceutical bioinformatics. We worked hard on a course book, which after a year got printed. It ended up with 400 pages, 15 chapters, and 3 appendices. It also includes examples on how to do discussed topics in Bioclipse:

The chapters are:
  1. Introduction
  2. Background
  3. Drug discovery and development
  4. Bioinformatics, drugs and omics
  5. Representing molecules in computers
  6. Representation of 3D structures
  7. Molecular descriptors
  8. Sequence analysis
  9. Macromolecular descriptors
  10. Design of experiments
  11. Data analysis
  12. Databases
  13. QSAR
  14. Proteochemometrics
  15. Semantic web
  16. Answers

And three appendices:
  A. Basic probability theory
  B. Basic matrix algebra
  C. Introduction to Bioclipse

The book is currently undergoing proof review and available to course participants only, and should become available in a couple of months for the general public.


  1. Hello Egon.... I am Anurag Passi, Project Assistant at OSDD, CSIR. I have just started working in the field of cheminformatics, and i was trying to understand what molecular descriptors are. I would be very grateful if you provide me with some basic study materials so that i can get to know basics in the molecular descriptors.

  2. What about signing up for the (free) course I mention in my post? The next one is in August, and if that is too late, I can recommend the book. See

    Otherwise, the Chemistry Development Kit is a good starting place. It can calculate many descriptors, you have access to the source code, etc, etc. Bioclipse has a good extension for calculating molecular descriptors too, and I suggest to check out this paper:

    And, if you have more detailed questions about open source molecular descriptor solutions, I can recommend the Blue Obelisk eXchange, which is a question-and-answer website:

    I hope this helps,


  3. sir,
    i am from india. can i apply for the pharmaceutical bioinformatics course at UPPSALA university for spring session. i have to pay the free or not. i have completed my

  4. Dear Mahender,

    Please contact Maris, who is the course leader. Full details can be found at this website: