Reliable and fast computation of protein free energy is crucial for protein-structure analysis, structure-based protein design and protein docking. Rigorous treatments based on physical effective energy functions involve computationally expensive methods such as free energy perturbation, which are time–consuming and are thus incompatible with the need to perform extensive scans. Commonly used fast methods, in turn, involve empirically derived scoring functions and usually do not include protein flexibility or are based on statistical potentials and are therefore highly dependent on the availability of case-dependent experimental training data. Hence, such methods are inherently limited in accuracy and applicability.

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