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Structural bioinformatics, or computational structural biology, is a large subject that encompasses, e.g., 3D structure prediction of proteins, function analyses and interactions between proteins as well as between proteins and ligands.
Molecular Dynamics Simulations
Main article: Molecular dynamics simulations
Molecular dynamics simulations enable studying motions in a molecular system at atomistic detail (or a more coarse grained scale). The required time scales depend on what is observed in the system, but a few hundred nanoseconds to a few microseconds is often possible to simulate in a reasonable time, depending on available hardware. It is a good complement to experimental techniques that can only give snapshots, or an average, of atom positions.
Main article: Molecular docking
Docking is commonly used to find out how molecules bind (non-covalently) to each other. Often the interactions between a small molecule and a protein is studied (protein-ligand docking), but two proteins can also be docked together (protein-protein docking) to discover their quartenary structure.
Main article: Visualization
Visualizing the 3D structure of a protein system may seem trivial, but it is important nonetheless. First one must decide what to draw and how to render it and finally there are many settings to produce an appealing image, or a movie, to present to others.
3D Structure Prediction
Main article: Structure prediction
Predicting the 3D structure of a protein based on its primary structure (amino acid sequence) is important since there are no published experimental structures for many important proteins and protein families.
BILS provides support, to research groups in Sweden, for setting up, running and analyzing molecular modelling computations. However, we cannot provide computational resources for all projects. We therefore recommend our clients to apply for access to compute resources from SNIC and run the calculations on their own allocations.
Magnus Lundborg, BILS