About MDockPeP2

The MDockPeP2 server predicts protein-peptide complex structures starting with the protein structure and the peptide sequence. A flowchart of the protocol is shown as following.



MDockPeP2 can be briefly divided into three stages.

1. In Stage 1, for a query peptide, a protein structure database is searched to find fragments sharing similar sequence. These fragments are used as templates to build peptide conformers.
   
2. In Stage 2, peptide conformers are generated and then independently docked to a target protein surface using a well-developed protein-protein docking program (global rigid docking). The generated models are further refined using a well-established protein-small molecule docking program (local flexible refinement).
   
3. In Stage 3, peptide conformers are merged and evaluated using a hybrid scoring function, which considers both calculated binding scores and interface similarities.
   
   

MDockPeP2 was evaluated based on the PepPro benchmarking database, containing 89 non-redundant protein-peptide complexes and 58 unbound protein receptors. The peptide sequence length varies from 5 to 29, and 46% of them are long peptides (longer than 15 residues).

More details about MDockPeP2 are available in the reference:

1. Xu X, Zou X. Predicting Protein-peptide complex structures by accounting for peptide flexibility and physicochemical environment. J. Chem. Inf. Model., 2022, 62: 27-39. DOI: https://doi.org/10.1021/acs.jcim.1c00836