Computational structural biology is a mature field of research whose contribution to life sciences is becoming increasingly more appreciated. The aim of this course is to provide a solid basis of computational structural biology methods, with an emphasis on practical protein modelling and simulation. Further, this course is designed to have a smooth learning curve regarding the GNU/Linux environment and its command-line interface. By the end of the course, the students are expected to master the three major computational structural biology methods – homology modelling, molecular dynamics, and protein docking – not only from a user perspective but also from a theoretical standpoint.