PatchDock and SymmDock: servers for rigid and symmetric docking

By Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson. 2005

2,889 citations recorded by the source corpus.

Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein–protein and protein–small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at . The methods behind the servers are very efficient, allowing large-scale docking experiments.

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

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In Computational Theory and Mathematics

1. Alexandre M. J. J. Bonvin
2. Shengyou Huang
3. Xiaoqin Zou
4. Jeffrey J. Gray
5. M. V. van Dijk
6. David Baker
7. D. Ritchie
8. Brian G. Pierce

In Materials Chemistry

1. Alexandre M. J. J. Bonvin
2. Jeffrey J. Gray
3. David Baker
4. Yang Zhang
5. Andrej Sali
6. D. Ritchie
7. Shengyou Huang
8. M. V. van Dijk

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. Jeffrey J. Gray
3. Shengyou Huang
4. David Baker
5. Xiaoqin Zou
6. Brian G. Pierce
7. Yang Zhang
8. Zhiping Weng

Citations in the corpus

• Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking. (2013, methodology): “NR-subset and SnugDock-H were used for this analysis and two docking methods were tested: ZDOCK (Chen et al., 2003) 623 Downloaded from https://academic.oup.com/peds/article-abstract/26/10/621/1512673 by guest on 27 July 2018 and PatchDock (Duhovny et al., 2002; Schneidman-Duhovny et al., 2005).”
• The RosettaDock server for local protein–protein docking (2008, methodology): “Several protein–protein docking servers are available on the Internet, including ClusPro (2), GRAMM-X (3) and ZDOCK (4) based on fast-Fourier transform methods for grid matching; PatchDock and SymmDock (5) based on shape complementarity principles and symmetry restrictions; and Hex based on spherica”
• FireDock: a web server for fast interaction refinement in molecular docking (2008, methodology): “The PatchDock server (http://bioinfo3d.cs.tau.ac.il/PatchDock/) includes an option for automatic redirection of the solution candidates to FireDock.”
• An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “25,36,37 Because of is simplicity and fast speed, shape complementarity-based scoring methods are commonly used in the initial filtering stage of many docking programs such as ZDOCK and 3D-DOCK.”
• HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry (2018, background): “Wolfson and colleagues developed a geometry-based docking algorithm for the prediction of cyclically symmetric complexes, which is referred to as SymmDock (21).”
• P HYSICS - INFORMED DEEP NEURAL NETWORK FOR RIGID - BODY PROTEIN DOCKING (2022, methodology): “Baseline We benchmark our method against PatchDock (Duhovny et al., 2002; Schneidman-Duhovny et al., 2005).”
• Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry (2016, methodology): “Furthermore, the RMSD-B 1 columns of this table show that SAM often gives considerably better quality solutions, with average RMSD values of 1.70 A˚ SAM , 2.09 A˚ for M-Zdock and 2.40 A˚ for SymmDock .”
• Flexible backbone assembly and refinement of symmetrical homomeric complexes (2018, methodology): “In Table 3, we compare the global docking performance of Rosetta SymDock and the new SymDock2 to four leading homomer docking methods recently tested by Yan et al: SymmDock (Schneidman-Duhovny et al., 2005), MZDOCK (Pierce et al.”
• Recent progress and future directions in protein-protein docking. (2008, methodology): “As an important step towards addressing this difficulty, Cerutti et al. [122] developed the ELSCA (energy by linear superposition of corrections approximation) knowledge-based potential method of including solvation effects into the linearised Poisson-Boltzmann/SurfaceArea (PBSA) electrostatic model”
• The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design (2017, methodology): “PatchDock recommends using 4.0 Å in protein–protein docking.”
• Protein–protein interaction and quaternary structure (2008, methodology): “Instead, other procedures generate a number of alternative conformations and perform ‘crossdocking ’ on the conformers (Schneidman-Duhovny et al. 2005a ; Grünberg et al. 2006 ; Krol et al. 2007).”
• 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), In-terEvDock2 (12), GRAMM-X (13), RosettaDock server (14), PatchDock (15), Hex server (16), 3D-Ga”
• Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (2021, neutral): “, 2017), PATCHDOCK5 (Mashiach et al., 2010; Schneidman-Duhovny et al., 2005), and HDOCK6 (Yan et al.”