A1 Journal article (refereed)
Getting Docking into Shape Using Negative Image-Based Rescoring (2019)


Kurkinen, S. T., Lätti, S., Pentikäinen, O. T., & Postila, P. A. (2019). Getting Docking into Shape Using Negative Image-Based Rescoring. Journal of Chemical Information and Modeling, 59(8), 3584-3599. https://doi.org/10.1021/acs.jcim.9b00383


JYU authors or editors


Publication details

All authors or editors: Kurkinen, Sami T.; Lätti, Sakari; Pentikäinen, Olli T.; Postila, Pekka A.

Journal or series: Journal of Chemical Information and Modeling

ISSN: 1549-9596

eISSN: 1549-960X

Publication year: 2019

Volume: 59

Issue number: 8

Pages range: 3584-3599

Publisher: American Chemical Society

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1021/acs.jcim.9b00383

Publication open access: Openly available

Publication channel open access: Partially open access channel

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/65419


Abstract

The failure of default scoring functions to ensure virtual screening enrichment is a persistent problem for the
molecular docking algorithms used in the structure-based drug discovery. To remedy this problem, elaborate rescoring and post-processing schemes have been developed with a varying degree of success, specificity, and cost. The negative imagebased rescoring (R-NiB) has been shown to improve the flexible docking performance markedly with a variety of drug targets.The yield improvement is achieved by comparing the alternative docking poses against the negative image of the target protein’s ligand-binding cavity. In other words, the shape and electrostatics of the binding pocket is directly used in the similarity comparison to rank the explicit docking poses. Here, the PANTHER/ShaEP-based R-NiB methodology is tested with six popular docking software, including GLIDE, PLANTS, GOLD, DOCK, AUTODOCK, and AUTODOCK VINA, using five validated benchmark sets. Overall, the results indicate that the R-NiB outperforms the default docking scoring consistently and inexpensively; i.e., demonstrating that the methodology is ready for wide-scale virtual screening usage.


Free keywords: drugs; molecular docking; PANTHER/ShaEP-based R-NiB methodology


Contributing organizations


Ministry reporting: Yes

Reporting Year: 2019

JUFO rating: 1


Last updated on 2021-09-06 at 03:41