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Methods
 MD SimulationsComputer simulations commonly used to study the temporal evolution of a system in question, based on Newtonian-mechanics, statistical-thermodynamics, and electrostatic approximations |  Dynamic Enssamble DockingA protocol developed in our lab, which combines all of the other computational methods used in our lab. Allows us to imitate the association process between proteins and estimate the free energy |  Molecular ModellingModelling protein structures in atomistic resolution based on sequence similarity as well as ab-initio folding, using different servers and software |
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 Normal Modes AnalysisThe system of interest is approximated through an Elastic Network Model (ENM) that considers the interatomic interactions as a network of mechanical springs (harmonic approximation). The eigenvalues and eigenvectors of the Hessian matrix of the atomic coordinates describe the collective motion of the protein, where each eigenvalue represents an individual frequency of the motion |  MDeNMKinetic energy is “injected” into the conformational space spanned by a linear combination of the low-frequency normal modes, which are attributed to large conformational changes in the protein. By so, the protein is able to overcome energetic barriers and to sample a large number of unique conformations, much more than attained by regular molecular dynamics simulations |  DockingA method to predict the structure of complexes between two proteins or a protein and its' ligand |
 Contact "Fingerprint"Analysis of critical residues which constitute the interface between proteins by calculating the geometric mean of the minimal distances, over the course of MD simulations |
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