Is there any correlation between molecule sizes and their interaction energy after a molecular docking?
We're trying to analyze some curious data about the energy on the interactions between amino-acids and some other molecules, like tRNAs and a peptidyl-transferase center. Does the size of the receptors alone influence on the energy resulting from the docking?
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João Rodrigues
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daniel.ancord •
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daniel.ancord •
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Short answer: yes. The more atoms you have the more interactions you will have accounted for by the scoring function, therefore, the more 'energy' you will have.
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See this article below:
http://www.sdsc.edu/pb/edu/pharm201/13/c27.pdf
especially pay attention to their formulas and Figures.