ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

By Brian G. Pierce, K. Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, Zhiping Weng. 2014

1,649 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling (2021, methodology): “ZDOCK is a fast and accurate FFT-based rigid-body docking method which utilizes pairwise statistical potentials; it is a staple method for benchmarking protein–protein docking performance (Pierce and Weng, 2008; Moal et al., 2013; Pierce et al., 2014; Wallner and Mirabello, 2017; Yan and Huang, 2019”
EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function (2019, methodology): “If the two chains are uploaded separately, the user is given an option to dock the two chains together using ZDOCK [31], a state-of-the-art fast Fourier transform-based protein-protein docking software.”
Performance and its limits in rigid body protein-protein docking (2020, neutral): “However, the other rigid body docking programs, including ZDOCK (Chen et al., 2003), GRAMM (Tovchigrechko and Vakser, 2005, 2006), pyDOCK (Cheng et al., 2007), and FTDock (Gabb et al., 1997) perform very similarly to ClusPro, and hence the latter can be used to explore the accuracy and limitations o”
Progress in molecular docking (2019, methodology): “[37] propose a new scoring function which combines pairwise shape complementarity(PSC) with desolvation and electrostatic and develop the ZDOCK server [38]”
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry (2018, background): “To make protein–protein docking user-friendly, a number of protein–protein docking servers such as ClusPro (4), HADDOCK (5), RosettaDock server (6), GRAMMX (7), 3D-Garden (8), HEX server (9), SwarmDock (10), ZDOCK server (11), PatchDock (12), ATTRACT (13), pyDockSAXS (14), InterEvDock (15) and HDOCK”
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, background): “A number of template-free docking servers have been developed and released to the public, such as ATTRACT (5), ClusPro (6), HADDOCK (7), ZDOCK server (8), SwarmDock (9), pyDockSAXS (10), pyDockWeb (11), InterEvDock2 (12), GRAMM-X (13), RosettaDock server (14), PatchDock (15), Hex server (16), 3D-Gar”
What Method to Use for Protein-Protein Docking? (2019, methodology): “ZDOCK [12] and pyDock [13] are rigid-body docking algorithms based on the use of fast Fourier transforms (FFTs), with pyDock built on the earlier FTDock method [18].”