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J Chem Inf Model. 2015 Mar 23;55(3):475-82. doi: 10.1021/ci500731a. Epub 2015 Feb 19.

Classification of current scoring functions.

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†State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, People's Republic of China.
§State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, People's Republic of China.


Scoring functions are a class of computational methods widely applied in structure-based drug design for evaluating protein-ligand interactions. Dozens of scoring functions have been published since the early 1990s. In literature, scoring functions are typically classified as force-field-based, empirical, and knowledge-based. This classification scheme has been quoted for more than a decade and is still repeatedly quoted by some recent publications. Unfortunately, it does not reflect the recent progress in this field. Besides, the naming convention used for describing different types of scoring functions has been somewhat jumbled in literature, which could be confusing for newcomers to this field. Here, we express our viewpoint on an up-to-date classification scheme and appropriate naming convention for current scoring functions. We propose that they can be classified into physics-based methods, empirical scoring functions, knowledge-based potentials, and descriptor-based scoring functions. We also outline the major difference and connections between different categories of scoring functions.

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