A comprehensive overview of ab initio protein-protein docking on APCset: a novel antibacterial protein complex 3D structure dataset
Diseases caused by bacterial infections become a critical problem in public heath. Antibiotic, the traditional treatment, gradually loses their effectiveness due to the resistance. Meanwhile, the antibacterial proteins or peptides attract more attention because of their broad spectrum and little harm to the host cells. Therefore, exploring effective and new antibacterial proteins is urgent and necessary. In this paper, we are committed to select the suitable docking methods for the structure modeling of the antibacterial protein complex. Firstly, we construct a three-dimensional (3D) structure dataset of antibacterial protein complexes for accurately evaluating the ability of docking methods, called APCset, which contains structures of 21 protein complexes whose receptors or ligands are homologous to antibacterial peptides from Antimicrobial Peptide Database (APD). Secondly, we summarize the key aspects of five ab initio docking methods, such as ZDOCK3.0.2, FRODOCK3.0, ATTRACT, PatchDock, and Rosetta. These five methods have respective advantages in search strategy and scoring function. On APCset, the top pose of ZDOCK is the best pose on the target of 14/21, and the predicted conformations are more accurate on nearly half (11/21) of the target in the top 5, compared with those of other methods. Most importantly, the computational efficiency of ZDOCK is half as fast as ATTRACT, which is the fastest one with an average running time of 6.174 minutes. Finally, we also assess five methods on Benchmark 5.0. Compared to other global docking methods, ZDOCK still yields better performance, with a success rate of 52.17% and an average hit count of 2.596 achieved when considering 1000 conformations according to the medium Critical Assessment of PRedicted Interactions (CAPRI) criteria. Our survey can offer insights into the exploration of effective antibacterial drugs by utilizing the appropriate docking methods, in order to support traditional antibiotics.
