Protein Docking（HDock）
1 Introduction
HDOCK1,2,3 uses a global search method based on Fast Fourier Transform (FFT) for sampling by a modified shape complementarity scoring method. During docking, one molecule (e.g. receptor) is fixed and the other molecule (e.g. ligand) is rotated uniformly in 3D Eulerian space. For each rotation of the ligand, the receptor and ligand are mapped onto a mesh and possible binding modes are exhaustively sampled in 3D translational space using the FFT method. The general case is rigid-body docking, although the flexibility problem can be handled indirectly by providing the residue information of the binding sites as constraints.
Figure 1. The overall architecture of HDock.
Figure 2. The performance of HDock.
2 Parameters
| Name | Description |
|---|---|
| partner1 | The PDB file of partner1 protein. |
| partner2 | The PDB file of partner2 protein. |
| spacing | Grid spacing for translation. |
| angle | Angle interval for rotation. |
| nmax | The number of output results. |
| rmsd | RMSD cutoff for clustering. |
| rsite | Residue bining site residues. |
| lsite | Ligand bining site residues. |
| restr | Distance constraints between interacting amino acids. |
3 Results Explanation
HDock predicts the conformation of the complex after docking with partner1 and partner2.
Including two types of files, the. pdb suffix file is the predicted complex conformation file, and score.csv is the HDock score for the predicted complex conformation, where the lower the score, the stronger the binding ability. The docking scores are calculated using the knowledge-based iterative scoring functions ITScorePR4 or ITScorePP5. A more negative docking score indicates a more likely binding model; however, the score should not be regarded as the true binding affinity between the two molecules, as it has not been calibrated against experimental data.
4 Reference
[1] Yan Y, Tao H, He J, Huang S-Y.* The HDOCK server for integrated protein-protein docking. Nature Protocols, 2020. https://doi.org/10.1038/s41596-020-0312-x
[2] Yan Y, Zhang D, Zhou P, Li B, Huang S-Y. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res. 2017;45(W1):W365-W373. https://doi.org/10.1093/nar/gkx407
[3] Yan Y, Wen Z, Wang X, Huang S-Y. Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking. Proteins 2017;85:497-512. https://doi.org/10.1002/prot.25234
[4] Huang S-Y, Zou X. A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Res. 2014;42:e55. https://doi.org/10.1093/nar/gku077
[5] Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579. https://doi.org/10.1002/prot.21949