TY - JOUR
T1 - Development of a New Scoring Function for Virtual Screening
T2 - APBScore
AU - Bao, Jingxiao
AU - He, Xiao
AU - Zhang, John Z.H.
N1 - Funding Information:
This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0501700, and 2019YFA0905201), the National Natural Science Foundation of China (Grant Nos. 21922301, 21761132022, 21673074, 91753103, and 21933010), and the Natural Science Foundation of Shanghai Municipality (Grant No. 18ZR1412600). We also thank NYU Shanghai and the Supercomputer Center of East China Normal University (ECNU Multifunctional Platform for Innovation 001) for providing computer resources.
Funding Information:
This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0501700, and 2019YFA0905201) the National Natural Science Foundation of China (Grant Nos. 21922301 21761132022, 21673074, 91753103, and 21933010), and the Natural Science Foundation of Shanghai Municipality (Grant No. 18ZR1412600). We also thank NYU Shanghai and the Supercomputer Center of East China Normal University (ECNU Multifunctional Platform for Innovation 001) for providing computer resources.
Publisher Copyright:
© 2020 American Chemical Society.
PY - 2020/12/28
Y1 - 2020/12/28
N2 - 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.
AB - 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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U2 - 10.1021/acs.jcim.0c00474
DO - 10.1021/acs.jcim.0c00474
M3 - Article
C2 - 33052694
AN - SCOPUS:85096067096
SN - 1549-9596
VL - 60
SP - 6355
EP - 6365
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 12
ER -