Models of the folding and binding in biomolecules are usually based on certain assumptions of additivities among free energies. For example, QSAR methods assume group additivities of free energies, and folding and docking algorithms assume free energies can be decomposed into terms for hydrogen bonds, hydrophobic interactions, van der Waals interactions, etc. Are these assumptions valid? Few methods have been available to test such assumptions. We have been developing models that are useful for testing additivity assumptions. The same kinds of models have been useful for setting standards for testing conformational search methods. Such modelling can be useful for indicating how to repair the flaws in current energy models and search strategies.
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