Zhang XJ, Jiang LL, Weng GQ, Shen C, Zhang O, Liu MQ, Zhang C, Gu SK, Wang JK, Wang XR, Du HY, Zhang H, Zhang K, Wang EC, Hou TJ. HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes. Nucleic Acids Research, 2025, gkaf379.[HTML]
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.[HTML]
Chu L-S, Ruffolo JA, Harmalkar A, Gray JJ. Flexible protein–protein docking with a multitrack iterative transformer. Protein Science, 2024, 33(2):e4862.[HTML]
Zacharias M. Protein–protein docking with a reduced protein model accounting for side-chain flexibility. Protein Science, 2003, 12(6):1271-1282.[HTML]
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.[HTML]
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.[HTML]
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.[HTML]
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.[HTML]
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.[HTML]
Wang E, Fu W, Jiang D, Sun H, Wang J, Zhang X, Weng G, Liu H, Tao P, Hou T. VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations. Journal of Chemical Information & Modeling, 2020, 60(11):5353-5365.[HTML]
Liu, X, Peng, L., Zhang, J. Z. H. Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants. Journal of Chemical Information & Modeling, 2019, 59(1):272-281.[HTML]