Computer based methods - Modeling and Simulation

Using a many different computer-based methods, a wide array of questions can be answered, ranging from static models to the influence of single-point mutations on the dynamics of a protein or even a complex of proteins. Thus, using …

… homology modeling, the structure of proteins at an atomistic level based on related proteins, which are already structurally known, can be predicted. Here, only knowledge of the sequence of the protein is necessary, while the quality of the model depends on its sequence similarity to structurally the known protein.

… molecular docking, the binding mode of small molecules to the active site or binding pocket of a protein, can be predicted.

… protein-protein docking, the orientation of proteins in complexes, can be predicted.

… Molecular dynamics (MD) simulations … 

• … the influence of proteins mutations on the dynamics of a protein or complex can be predicted.
• … the binding pathway and binding spot of ligands in proteins can be predicted.
• … the affinity of ligands or proteins binding to proteins can be predicted.
• … the folding of small peptides can be predicted.

… virtual screening, new leads for drug development can be predicted.