Computational Chemistry and Molecular Modelling Basics
Computational modelling has gained an increasingly important role in biochemical and biomolecular sciences over the past decades. This is related to significant developments in terms of methodology and software, as well as the amazing technological advances in computational hardware, and fruitful connections across different disciplines. Today, we readily screen virtual libraries of several million compounds searching for potential new inhibitors, run simulations of large biomolecular complexes in micro or even millisecond timescales, or predict protein structures with similar accuracy to high-resolution X-ray crystallography. In this introductory chapter, the basics of biomolecular modelling are outlined, to help set the foundation for the subsequent, more specialised chapters. In order for the chapter to be ‘readable’ to interested researchers and PhD students in the biochemical and biomolecular fields our aim has been to do so without weighing down the text with too much detailed mathematics—yet at the same time providing a sufficient level of theory so as to give an understanding of what is implied when talking about molecular dynamic simulations, docking or homology modelling.