Docking‑based virtual screening of BRD4 (BD1) inhibitors: assessment of docking methods, scoring functions and in silico molecular properties.

ABSTRACT: To enhance the accuracy of virtual screening for bromodomain-containing protein 4 (BRD4) inhibitors, two docking protocols and seven scoring functions were compared. A total of 73 crystal structures of BRD4 (BD1) complexes were selected for analysis. Firstly, docking was carried out using both the LibDock and CDOCKER methods. The CDOCKER protocol was shown to be more effective based on the root mean square deviation (RMSD) values (in Å) between the docking positions and the co-crystal structures, achieving a docking accuracy rate of 86.3%. Then, among the various scoring functions (LigScore1, LigScore2, PLP1, PLP2, PMF, PMF04 and Ludi3), PMF showed the highest correlation with inhibition constants (r² = 0.614), while Ludi3 scored lowest (r² = 0.266). Finally, using li

SUBMITTER: Dong J 

PROVIDER: S-EPMC11657568 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature