Liu Group
Result Example

P3DOCK is a hybrid docking method based on free and template-based docking. For free docking, it employs 3dRPC which takes into account protein/RNA geometric and eletrostatic complementarity. For template-based docking, it uses PRIME which employs TMalign to align protein and RMalign to align RNA to search templates and build models.
First, the protein and RNA structures that you want to dock must be provided by the following two ways:
  • 1. Provide a PDB id. If you provide structure by this way, the webserver will fetch the structure from PDB.
  • 2. Upload a file
  • Second, the chain id must be assigned.
    Parameters configure:
    The detail parameters of P3DOCK also can be set. However, we would not suggest changing the default parameters.
  • If you have the native structure and want to calcaulate the RMSD. Please provide the native structure and assign the chain id(default false).
  • The models can be sorted by TM-score (default) and TR-score.
  • The score cutoff can be set as a float value between 0 and 1(default 0.35). Please noted that models that less than cutoff will be discarded.
  • model number: the number of complexes with pdb format output by P3DOCK.
  • docking type: template-based or hybrid (default template-based docking).

  • References:
    1. Jinfang Zheng, Xu Hong, Juan Xie, Xiaoxue Tong, Shiyong Liu. P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking. Bioinformatics
    2. Jinfang Zheng, Petras J.Kundrotas, Ilya A.V akser and Shiyong Liu. Template-based modeling of protein-RNA interactions. PLOS Computational Biology
    3. Yangyu Huang, Shiyong Liu, Dachuan Guo, Lin Li, Yi Xiao. A novel protocol for three-dimensional structure prediction of RNA-protein complexes. Scientific reports