IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

Abstract

BackgroundProtein-protein docking is an in silico method to predict the formation of protein complexes. Due to limited computational resources, the protein-protein docking approach has been developed under the assumption of rigid docking, in which one of the two protein partners remains rigid during the protein associations and water contribution is ignored or implicitly presented. Despite obtaining a number of acceptable complex predictions, it seems to-date that most initial rigid docking algorithms still find it difficult or even fail to discriminate successfully the correct predictions from the other incorrect or false positive ones. To improve the rigid docking results, re-ranking is one of the effective methods that help re-locate the correct predictions in top high ranks, discriminating them from the other incorrect ones.In this paper, we propose a new re-ranking technique using a new energy-based scoring function, namely IFACEwat - a combined Interface Atomic Contact Energy (IFACE) and water effect. The IFACEwat aims to further improve the discrimination of the near-native structures of the initial rigid docking algorithm ZDOCK3.0.2. Unlike other re-ranking techniques, the IFACEwat explicitly implements interfacial water into the protein interfaces to account for the water-mediated contacts during the protein interactions.ResultsOur results showed that the IFACEwat increased both the numbers of the near-native structures and improved their ranks as compared to the initial rigid docking ZDOCK3.0.2. In fact, the IFACEwat achieved a success rate of 83.8% for Antigen/Antibody complexes, which is 10% better than ZDOCK3.0.2. As compared to another re-ranking technique ZRANK, the IFACEwat obtains success rates of 92.3% (8% better) and 90% (5% better) respectively for medium and difficult cases. When comparing with the latest published re-ranking method F2Dock, the IFACEwat performed equivalently well or even better for several Antigen/Antibody complexes.ConclusionsWith the inclusion of interfacial water, the IFACEwat improves mostly results of the initial rigid docking, especially for Antigen/Antibody complexes. The improvement is achieved by explicitly taking into account the contribution of water during the protein interactions, which was ignored or not fully presented by the initial rigid docking and other re-ranking techniques. In addition, the IFACEwat maintains sufficient computational efficiency of the initial docking algorithm, yet improves the ranks as well as the number of the near native structures found. As our implementation so far targeted to improve the results of ZDOCK3.0.2, and particularly for the Antigen/Antibody complexes, it is expected in the near future that more implementations will be conducted to be applicable for other initial rigid docking algorithms.

InCoB2014: bioinformatics to tackle the data to knowledge challenge

“…The biological function of a protein is ascribed to its 3D structure and five papers [ 6 - 10 ] provide updates on structural bioinformatics research. At the outset, for proteins that have neither experimental structural information nor structural homologues, predicting the 3D structure of a protein continues to remain a challenge.…”

“…For multi-domain proteins, the domain boundaries may be delineated by identifying inter-domain linker regions [ 8 ], for subsequent prediction of domain 3D structures using either [ 6 ] or [ 7 ]. Liu et al [ 9 ] have analysed all available protein 3D structures and developed a new approach to discriminate between biologically relevant protein interactions and crystal packing contacts, while IFACEwat by Su et al [ 10 ] seeks to predict near native structures of protein-protein complexes with the inclusion of solvent molecules at the interface.…”