Depending on the size of your trajectory, you may want to increase this -step. The above command will calculate the network for every 100th frame in the trajectory. pdb - threshold 7.0 - step 100 - generate - plots - calc - BC - calc - L - discard - graphs - lazy - load wt. Given a trajectory called wt.dcd and a topology file called wt.pdb, the following command could be used:Ĭalc_network. Try increasing the distance threshold when this happens. When this is not the case, an error will occur. Note: for -calc-L to work, all nodes in the network must be accessbile from all other nodes in the network. previous studies have suggested that positions that result in high delta L values may steer conformational changes. This may indicate that the mutation has an important effect on protein function e.g. A mutation may result in a change in L of a number of residues in the protein. This can be used to, for example, analyze SNPs. The average shortest path to a residue gives an idea of how accessible the residue is within the protein. The average shortest path (L) to a given residue is calculated by working out all the shortest paths to the given node and dividing by the number of paths. Residues in a protein that have a high BC reveal locations that tend to be important for controlling inter-domain communication in a protein. It is equal to the number of shortest paths from all vertices to all others that pass through that node. Comparing changes in BC and L between the simulation of a wild-type and mutant protein can provide interesting insights into differences in intra-protein communication, which can affect the function of the protein.īetweenness centrality (BC) is a measure of how important a residue is for communication within a protein. RINs can also be useful in the analysis of SNPs. This can be used to determine which residues are important for intra-protein communication and conformational changes. Currently, MD-TASK can be used to analyze the change in betweenness centrality (BC) and average shortest path (L) of residues in a protein over a molecular dynamics simulation. Once the network has been constructed, there are various network measures that can be used to analyze it. MD-TASK considers an interaction between two residues to exist if the beta carbon atoms of the residues are within a user-defined cut-off distance (usually around 6.5 – 7.5 Å) of each other. An edge (or connection) between two nodes exists if there is an interaction between the two residues those nodes represent. In a RIN, each residue in the protein is a node in the network. Residue Interaction Networks (RIN) are analyzed using a branch of Mathematics known as graph theory.
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