Sérgio F. Sousa and Henrique S. Fernandes (BioSIM) presented a 4 h seminar to the students of the M.Sc. in Computational Biology, University of Coimbra. In this seminar, which took place on April 7th, with the title “QM/MM Methods and Protein Ligand Docking: Fundamentals and Applications”, Sérgio F. Sousa and Henrique Fernandes presented an introduction to this field of research. This was illustrated with recent examples developed at BioSIM.