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

Su C, Nguyen TD, Zheng J, Kwoh CK - BMC Bioinformatics (2014)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Protein-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.

Results: Our 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.

Conclusions: With 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.

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Related in: MedlinePlus

Overview of the IFACEwat implementation.
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Related In: Results  -  Collection

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Figure 6: Overview of the IFACEwat implementation.

Mentions: in which the ScoreIFACE is derived from the combination of shape complementarity, electrostatics, and desolvation (SC+ELEC+DEIFACE using the interface Atomic Contact Energy IFACE) employed in the initial rigid docking algorithm of ZDOCK3.0.2. The ELJ_repulsive and Ewater-mediated-Hbond are Lennard-Jones repulsive and water-mediated Hydrogen bond energies respectively to represent the protein-water interactions. Finally the ΔGinterface is the free energy change of the interface representing the interactions between the protein partners. The four parameters w1, w2, w3, and w4 are separate weights of the corresponding potentials. Flowchart of the whole process is shown in Figure 6.


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

Su C, Nguyen TD, Zheng J, Kwoh CK - BMC Bioinformatics (2014)

Overview of the IFACEwat implementation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4290663&req=5

Figure 6: Overview of the IFACEwat implementation.
Mentions: in which the ScoreIFACE is derived from the combination of shape complementarity, electrostatics, and desolvation (SC+ELEC+DEIFACE using the interface Atomic Contact Energy IFACE) employed in the initial rigid docking algorithm of ZDOCK3.0.2. The ELJ_repulsive and Ewater-mediated-Hbond are Lennard-Jones repulsive and water-mediated Hydrogen bond energies respectively to represent the protein-water interactions. Finally the ΔGinterface is the free energy change of the interface representing the interactions between the protein partners. The four parameters w1, w2, w3, and w4 are separate weights of the corresponding potentials. Flowchart of the whole process is shown in Figure 6.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Protein-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.

Results: Our 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.

Conclusions: With 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.

Show MeSH
Related in: MedlinePlus