The course

What is bioinformatics?

Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze, and integrate biological and genetic information which can then, for example, be applied to gene-based drug discovery and development. Bioinformatics is, again just as an example, essential for the use of genomic information in understanding human diseases or in the identification of new molecular targets for drug discovery.

In the context of chemistry, bioinformatics is often used together with cheminformatics (the informatics of non-biological, normally small molecules). This course will occasionally mention some aspects of cheminformatics, but the focus will be on aspects of bioinformatics that are relevant for chemists and chemistry.

Topics of the course

Bioinformatics is just as wide a description as chemistry. There is no way you can say what is chemistry, and it is equally impossible to say what is bioinformatics.

Figure 1. Bioinformatics is broad. So broad that it is impossible to mention all sub-topics. We will have to limit ourselves to the introduction of a series of concepts behind tools commonly used, and the most widely used and most broadly applicable methods: Force Fields.

This course is meant for chemists and natural scientists, and the topics of this course have been chosen accordingly; we will discuss in silico drug design because this area is the worlds largest employer for computational chemists:

• The computational core of in silico drug design is drug docking .
• Drug design needs protein structures that can often be predicted using homology modelling, which in turn needs structure validation.
• Proteins are not solids but highly mobile things so we will need to discuss Molecular Dynamics/ Energy calculations .
• All these topics use Force Fields (FF), and therefore Force Fields will be the red thread through this course.
• Finally, many of the things we will discuss use concepts of evolution theory that we will discuss using (multiple) sequence alignment and analyses as example.

These topics will be pursued through a series of six seminars that each come with associated texts, videos, and practical exercises. Further explanation concerning the topics, seminars and their coherence are listed in the table below, and in the next few section.

Figure 2. All these topics use Force Fields (FF) and therefore Force Fields will be the red thread through this course.