Abstract
In this study, we developed a new physical-based scoring function, Atom Pair-Based Scoring function (APBScore), which includes pairwise van der Waals (VDW), electrostatic interaction, and hydrogen bond energies between the receptor and ligand. Despite the simple form of this scoring function, the tests of APBScore on several benchmark datasets show its excellent performance in scoring as compared to other widely used traditional scoring functions. Particularly, the scoring performance of APBScore is among the top-ranking scoring functions for complexes with zinc/ligand interactions. In addition to the scoring power, APBScore also shows good performance in ranking and docking as compared to some traditional scoring functions. In addition, the APBScore is sensitive to receptor/ligand atomic collisions and therefore can correctly identify decoy complex structures with atomic collisions. These features are the result of optimizing atom-pair VDW interactions, performing structural minimization of the initial structures, and treating zinc/ligand interactions more accurately. The source code of APBScore is available at https://github.com/BaoJingxiao/APBScore.
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