Weng GQ, Wang EC, Wang Z, Liu H, Li D, Zhu F, Hou TJ. HawkDock: a web server to predict and analyze the structures of protein-protein complexes based on computational docking and MM/GBSA. Nucleic Acids Research, 2019, 47(W1): W322-W330.pdf

If you use HawkDock, please also cite:

Zacharias M. Protein–protein docking with a reduced protein model accounting for side-chain flexibility. Protein Science, 2003, 12(6):1271-1282.pdf

Feng T, Chen F, Kang Y, Sun HY, Liu H, Li D, Zhu F, Hou TJ. HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. Journal of Cheminformatics, 2017, 9(1):66.pdf

Hou TJ, Qiao XB, Zhang W, Xu XJ. Empirical Aqueous Solvation Models Based on Accessible Surface Areas with Implicit Electrostatics. Journal of Physical Chemistry B, 2002, 106(43):11295-11304.pdf

If you use MM/GBSA, please also cite:

Hou TJ, Wang JM, Li YY, Wang W. Assessing the performance of the MM/PBSA and MM/GBSA methods: I. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information & Modeling, 2011, 51(1):69-82.pdf

Sun HY, Li YY, Tian S, Xu L, Hou, TJ. Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Physical Chemistry Chemical Physics, 2014, 16(31):16719-16729.pdf

Chen F, Liu H, Sun HY, Pan PC, Li YY, Li D, Hou TJ. Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Physical Chemistry Chemical Physics, 2016, 18(18):22129-22139.pdf