SwarmDock: a server for flexible protein-protein docking

By Mieczyslaw Torchala, Iain H. Moal, Raphael A. G. Chaleil, Juan Fernández-Recio, Paul A. Bates. 2013

261 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, methodology): “This set contained 56,015 docking models for 118 targets from the protein-protein docking Benchmark 4.0 [17], constructed using SwarmDock [18] gra-ciously provided by the authors of Moal et al [13].”
What Method to Use for Protein-Protein Docking? (2019, methodology): “SwarmDock [14,15] is a flexible docking method which uses a population-based memetic algorithm to optimize parameters characterizing the orientation, position, and conformations of protein subunits.”
Performance and its limits in rigid body protein-protein docking (2020, unknown): “, 2010) that are similar to ClusPro, and the servers SwarmDock (Moal et al., 2018; Torchala et al., 2013), and HADDOCK (High Ambiguity Driven DOCKing) (de Vries et al.”
Protein complex prediction with AlphaFold-Multimer (2021, background): “Traditional approaches to multimeric structure prediction have tended to rely on a hybrid of templatebased modelling and free docking [15, 16, 17, 18].”
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), GRAMM-X (7), 3D-Garden (8), HEX server (9), SwarmDock (10), ZDOCK server (11), PatchDock (12), ATTRACT (13), py-DockSAXS (14), InterEvDock (15) and HDO”
Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2 (2015, methodology): “10 predictions, and 40-67% for the top 100 predictions, comparable to the success rates on version 4 of the docking benchmark using SwarmDock and ZDOCK [37,38].”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “0 [106], using the SwarmDock algorithm [107-109], is presented here.”
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (2021, methodology): “Protein docking methods (Chen et al., 2003; Venkatraman et al., 2009; De Vries et al., 2010; Biesiada et al., 2011; Torchala et al., 2013; Schindler et al., 2017; Weng et al., 2019; Sunny and Jayaraj, 2021; Christoffer et al., 2021; Yan et al., 2020) typically run several steps: first, they sample t”
Software for molecular docking: a review (2017, methodology): “In the human predictor category, HADDOCK (Dominguez et al. 2003) was given the first rank, followed by SwarmDock (Venkatraman and Ritchie 2012).”
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, methodology): “As for the seven proteins in CASP13, taking the top 5 hits as the criterion, HawkDock could provide acceptable models for two targets (T152 and T153), compared with acceptable models for one target (T152) provided by LZERD (45) and acceptable models for two targets (T152 and T153) provided by other ”