While performing protein-protein docking using Haddock, the results included something called restraints violation energy and this value was a positive value. What is this energy and what is its significance in molecular docking?
Hi Manan,
HADDOCK will try to model your complex based on experimental/prediction information that you submitted as restraints. If a restraint is satisfied (distance, dihedral angle, RDC, etc) then the violation energy is 0, otherwise it's a positive number. So, technically, you'll want a number as close to 0 as possible.
However, in practice, if you have plenty of restraints (often) this value will not be 0 but slightly positive, meaning that some of your restraints were not completely respected (e.g. residues 2 and 4 are at 2.2Å instead of 2Å as specified in the restraint). If, however, the value is quite large, it means likely that there is something wrong with your restraints that makes them impossible to be satisfied.
Best,
João
Hi Manan,
HADDOCK will try to model your complex based on experimental/prediction information that you submitted as restraints. If a restraint is satisfied (distance, dihedral angle, RDC, etc) then the violation energy is 0, otherwise it's a positive number. So, technically, you'll want a number as close to 0 as possible.
However, in practice, if you have plenty of restraints (often) this value will not be 0 but slightly positive, meaning that some of your restraints were not completely respected (e.g. residues 2 and 4 are at 2.2Å instead of 2Å as specified in the restraint). If, however, the value is quite large, it means likely that there is something wrong with your restraints that makes them impossible to be satisfied.
Best,
João
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