Recently I have been using Swiss dock to evaluate in silico enzyme catalysis of hydrolase family! Out of all docking software, I, prefer swiss dock for its ease of use and quick result generation.
Swill dock gives results in full fitness and delta G values. I know delta G is the Gibbs free energy and the lower it is the better it is. One thing I am really confused about is what is full fitness? what does it mean? is it the binding affinity of a protein towards its substrate/ligand?
Is full fitness more important or less important than delta G, Or does delta G hold more importance over full fitness? or are they both equal in importance?
The ease of use and the fast execution are two double-edged swords. If the source code is not available, the swords are hiltless and the swordsman blind-folded.
Dear Suraj Mali I have already gone through that article yet I have not been able to find a singoe mention of full fitness or delta g.
Cheers
May I suggest the works of Grosdidier et al.: "EADock: Docking of Small Molecules Into Protein Active Sites With a Multiobjective Evolutionary Optimization" (2007) and "SwissDock, a protein-small molecule docking web service based on EADock DSS" (2011).
Cit.: "The FullFitness of a cluster is calculated by averaging the 30% most favorable effective energies of its elements, in order to limit the risk of a few complexes penalizing the whole cluster. This effective energy is written as the sum of the total energy of the system and a solvation term."
More info is reported in the papers.
Hope this help.
Kartik Puri
The full fitness of a cluster is calculated by averaging the 30% most favorable effective energies of its elements, in order to limit the risk of a few complexes penalizing the whole cluster.
Ref.: Article EADock: Docking of small molecules into protein active sites...
How the delta G is being calculated in SwissDock? I understand we can calculate the full fitness using the given equation in the paper. Can anyone please provide me any direction to delta G?
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