The RosettaDock server for local protein–protein docking

By Sergey Lyskov, Jeffrey J. Gray. Nucleic Acids Res., 2008

586 citations recorded by the source corpus.

The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.

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

View Paper: https://www.semanticscholar.org/paper/98c422932c5dc6e784909a617974d9cfc61ef13f

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Citations in the corpus

Finding correct protein–protein docking models using ProQDock (2016, unknown): “…approaches have been applied to this problem ranging from composite scoring describing the physics (Dominguez et al., 2003; Cheng et al., 2007; Lyskov and Gray, 2008; Pierce and Weng, 2007, 2008) to methods derived from the statistics of structural databases (Geppert et al., 2010; Liu and…”
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions (2011, background): “While a plethora of web servers is available for the docking of a pair of globular proteins [e.g. RosettaDock (16), HADDOCK (17), PatchDock (18), ClusPro (19) and more; see CAPRI (20)], these are not intended for the docking of peptides.”
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”
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers (2014, methodology): “To facilitate protein-protein docking prediction, web-based servers have been developed for rigid-body docking (Ritchie and Venkatraman, 2010; Tovchigrechko and Vakser, 2006), flexible docking and refinement (Lyskov and Gray, 2008; Mashiach, et al., 2010; Torchala, et al., 2013),”
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, background): “Some free docking servers include specific features such as symmetric docking (SymmDock (9), ZDOCK); local docking around an initial guess (RosettaDock (19), re-”
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta (2010, unknown): “To make these protocols more accessible, a number of web-based servers have been constructed, such as Robetta (Chivian et al., 2004), RosettaDock (Lyskov and Gray, 2008) and RosettaAntibody (Sivasubramanian et al., 2008).”
Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, background): “The server produces 1000 structures and returns details for the 10 lowest-energy models ( 50 ).”
RosettaAntibody: antibody variable region homology modeling server (2009, background): “Docking calculations can be done on several publicly available servers (31–38) including the RosettaDock Server (local docking only for high-resolution refinement, http://rosettadock.graylab.jhu.edu) ( 39 ).”
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”
Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE) (2018, unknown): “51,59 Tox dock.”
The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “Among those, only PatchDock/FireDock and the RosettaDock server can deal with structural flexibility but only at the side chain level.”
HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy (2017, unknown): “For years, a number of docking algorithms and their web servers such as ClusPro (10), HADDOCK (11), Roset-taDock server (12), GRAMM-X (13), 3D-Garden (14), HEX server (15), SwarmDock (16), ZDOCK server (17), PatchDock (18), ATTRACT (19), pyDockSAXS (20), In-terEvDock (9) and NPDock (21), have been…”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “docking strategy [55,61,62,67,115], the differential scoring performances shown here suggest a role for flexibilitydependent scoring functions, that may be used in conjunction with methods for predicting flexibility [116-120].”
A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum (2013, methodology): “Thus, to prepare mNeonGreen C-terminal fusions (number of linker amino acids in parenthesis), the following digests were performed: annexin A4 (12), NheI and BspEI (Alen Piljic, EMBL, Heidelberg, Germany; NM_001153.”