Technical Bulletin

The use of computers for predicting the structures and properties of biomolecules has closely paralleled computer development since the 1950s, and has been one of the core areas of theoretical or computational chemistry for the past 30 years. Initially, the focus was on force-field-based methodologies for studying the structures, dynamics, and interactions of biomolecules as such, and the development of accurate models for the main biological solvent, water. With the emergence of accurate quantum chemical techniques suitable for studying (from a quantum chemistry perspective) large systems, density functional theory entered the stage in the 1990s as the key approach for investigating enzymatic mechanisms or properties and reactions of small, but biologically relevant, molecules. The combined use of these tools, so-called QM/MM and lately QM/MM-MD techniques enables precise descriptions of biological phenomena and reactions.

With the exponential increase in data to be analyzed, obtained through the introduction of automated whole-genome and protein sequencing techniques, the field of bioinformatics rapidly emerged in the early 2000s from the pioneering laborious mapping and comparison of protein and gene sequences in molecular biology, via an intense phase, which to a large extent can be viewed as ‘database mining’ and the development of efficient computer-based algorithms, into a science of its own, which today has reached a high level of maturity and sophistication. Tools in bioinformatics are nowadays used with great success in structural biology, computational chemistry, genetics, molecular biology, the pharmaceutical industry, pharmacology, and more. The technical bulletin of bioinformatics and computer science included herein focus on protein structure determination (often referred to as homology modelling), and the tools of database screening and prediction used in drug design.

Here, a brief outline of simulation techniques are given, focusing on the interface between biology and medicinal chemistry; that is molecular mechanics/molecular dynamics to explore the evolution of a system, homology modelling to determine protein structures, and the use of bioinformatics tools such as molecular docking and pharmacophores in drug design. The aim is to provide a brief introduction to a vast and rapidly growing field.

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