Structural Bioinformatics

Structural Bioinformatics comprises the theory, methods and applications of bioinformatics and applies these to biological structure data. In other words, structural bioinformatics allows researchers to analyse and simulate 3D structures of molecules, as is facilitated by computer power. Since the 3D structure and function of molecules are two sides of the same coin, analysis and prediction of structure not only have structural implications, it allows the interpretation and extrapolation to functional properties of these molecules as well. Structural Bioinformatics is in essence a generic method, but is in practice applied most to the study of biologically active molecules: proteins, glycans, nucleic acids, lipids, peptides and small molecules. Structural Bioinformatics take advantage of the large amount of experimentally determined, high resolution 3D structures that are available from public databases, to either directly study structures, or to provide model structures for molecules or complexes thereof for which no experimental structures exist. These techniques are likewise applied in biological and pharmaceutical contexts, and by utilization of computational methods and structural bioinformatics, we can significantly reduce the time and cost invested in drug discovery and development campaigns. Few examples of techniques and their possibilities are:

• Structure analysis: allows inspection of protein structures and for instance prediction of mutational effects (to be used e.g. in protein engineering)
• Docking: provides 3D structures of complexes between protein and its binding partner (e.g. small compounds, peptides, proteins, glycans, lipids, and nucleic acids) which allows the prediction and investigation of interaction between molecules
• Molecular Dynamics Simulation: allows insight into motion of molecules and their complexes and stability of these, including calculation of binding free energies to predict the strength of the binding interactions between complexes e.g. protein-ligand complexes.
• Virtual Ligand Screening: allows the discovery of molecular entities as inhibitors or activators
• Ligand Optimisation: optimization of molecules with desired properties. This step involves direct binding assessment through ITC or SPR, or analysis through DSC. These biophysical methods and knowhow are provided by the platform.

Managers: Dr Gerry Nicolaes and Dr Kanin Wichapong