MDockPP

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The MDockPP Online Server provides structure predicitons for protein-protein, protein-RNA, and protein-DNA complexes. In addition to the common asymmetric heterodimeric docking, we extend our service to include homo-oligomeric docking for complexes of cyclic and dihedral symmetry. Moreover, in either the heterodimeric or homo-oligomeric docking, the asymmetric unit or the monomeric structure can actually contain multiple protein and nucleic acid molecules. In the case where the structures of the docking components are not availiable, the user can provide the primary sequences and the server will use AlphaFold2 to construct the monomeric structures for docking. The docking algorithm is based on Fast Fourier Transform (FFT), and a 6 degree rotational angle interval is used. The docking program is implemented on a single NVIDIA GeForce RTX 2080 Ti GPU to greatly improve its speed and achieve high accuracy. The docking results will be reassessed with our in-house scoring functions (ITScorePP for protein-protein interaction, ITScorePR for protein-RNA interaction, and ITScorePD for protein-DNA interaction) before reporting to users. Furthermore, we let users incorporate experimental information into the docking by setting constraining conditions on the binding partners. The users can block specific residues or bases from the binding interface, demanding specific residues or bases to be near the binding interface, or enforce specific pair interactions between specific residues or bases. The performance of our docking program has been tested repeatedly in CAPRI contests, which are community-wide competitions on protein-protein structure prediction, and bonafide scientific researches. Most recently, the MDockPP server won the first place in the CASP14/CAPRI50 competition. For more details, the reader is refered to the references [1-4].

[1] Huang, S. Y., Zou, X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 72: 557-579, 2008.
[2] Huang, S. Y., Zou, X. MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins 78:3096-3103, 2010.
[3] Huang, S. Y., Yan, C., Grinter, S. Z., Chang, S., Jiang, L., Zou, X. Q. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI. Proteins: Structure, Function and Bioinformatics, Special issue on 5th CAPRI Evaluations, 81:2183-2191, 2013.
[4] Duan, R., Qiu, L., Xu, X., Ma, Z., Merideth, B.R., Shyu, C.R., Zou, X. Performance of Human and Server Prediction in CAPRI rounds 38-45. Proteins: Structure, Function and Bioinformatics, 88:1110-1120, 2020.

If you uploaded primary sequences for structure prediction, please cite AlphaFold2 as well.
[5] Jumper, J., Evans, R., Pritzel A., et al. Highly accurate protein structure prediction with AlphaFold. Nature. 596:583-589, 2021.

Job Submission:

(Please be aware that due to the availability of GPU, jobs starting from sequences on our server may experience a waiting time of several days. We apologize for any inconvenience this may cause and appreciate your patience as we work to allocate necessary resources for your job to proceed.)

(Notice: The "Start From Sequence" section is currently under maintenance.)