Course overview for course in Pharmaceutical Bioinformatics

Learning Outcomes

The course will provide introduction to the area of chemobioinformatics in relation to drugs, omics, chemical biology, protein function, and biomedicine, which includes databases, sequence analysis, proteins and their interactions, chemical descriptions of proteins and organic compounds, data modeling, QSAR modeling, proteochemometrics modeling, drug discovery and development and use of chemobioinformatics software.

After a successful course completion, you will be able to :

  • understand and describe how chemobioinformatics tools can be used in biomedical and pharmaceutical research
  • use bio- and chemoinformatics programs for e.g. sequence alignment, 3D visualization, and advanced structure-activity relationship modeling methods such as proteochemometrics
  • seek relevant information in biological and chemical databases
  • calculate the chemical properties (descriptors) of potential drugs and target proteins, and correlate these to biological activities through chemobioinformatics modeling
  • apply experimental design to increase the outcome of your experiments at reduced cost and reduced experimental effort
  • interpret and validate the results of above-mentioned methods
  • use the Bioclipse chemobioinformatics workbech (software free of charge)


1. Introduction to Pharmaceutical Bioinformatics; 2. Pharmaceutical Bioinformatics – a Course Overview; 3. Representing Molecules in Computers; 4. Databases in Pharmaceutical Biosciences; 5.Statistical Experimental Design; 6. Structure Descriptors, Physical and Chemical; 7. Data Macromolecular Descriptors; 8. Alignments in Bioinformatics; 9. Representation of 3D structures; 10. Methods for Data Analysis; 11. QSAR and Proteochemometrics; 12. Validation of Models; 13. Lead Identification and Optimization; 14. Bioclipse tutorials and exercises


The course includes audiovisual presentations, written lecture notes, and down-loadable materials. Each lecture is accompanied with exercises and/or assignments, which are checked by the teacher who gives individual feedback to each student. Communication between participants and teachers takes place via the web and via email. The web-based teaching platform is also utilized for group exercises, discussions and assignments. Thus, the participants have contact with the teachers online throughout the course to ask questions and get clarifications.


Written examination through the website after a successful completion of the mandatory assignments.

Course literature

Introduction to Pharmaceutical Bioinformatics, Wikberg at al., 2011, Oakleaf Academic Publishing House, ISBN 978-91-979403-0-6
(inquiries at

Other materials and software is available for downloading during the course for complementary purpose.

Teaching Staff

Maris Lapins, PhD; Jarl Wikberg, Prof., MD, PhD; Ola Spjuth, PhD; Martin Eklund, PhD; Valentin Georgiev, PhD