ClusPro: a fully automated algorithm for protein-protein docking

By Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho. Nucleic Acids Res., 2004

832 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5130002a1d2a1007a7efba021ffaee7e690bf14b

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Citations in the corpus

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”
The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design (2017, methodology): “ClusPro 9 is another well-known docking server and was the first web-based antibody–antigen docking program publicly available.”
HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy (2017, neutral): “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…”
HexServer: an FFT-based protein docking server powered by graphics processors (2010, neutral): “ClusPro (7), GRAMM-X (8) and ZDOCK (9).”
The HDOCK server for integrated protein–protein docking (2020, background): “A number of docking servers, such as ClusPro 38,39 , HADDOCK 10 – 12 , GRAMM-X 40 , 3D-Garden 41 , HEX 42 , SWARMDOCK 43 , ZDOCK 44 , PatchDock 45 , RosettaDock 46 , ATTRACT 47 , pyDockWEB 48,49 , pyDockSAXS 50 , InterEvDock 13 and NPDock 51 , have been developed in the past decade.”
New additions to the ClusPro server motivated by CAPRI (2017, methodology): “These are (1) accounting for SAXS data in docking; (2) the option of considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers.”
PatchDock and SymmDock: servers for rigid and symmetric docking (2005, background): “However, only a few algorithms are currently available as a free web service [the pioneer was the ClusPro server (19)].”
FireDock: a web server for fast interaction refinement in molecular docking (2008, background): “ClusPro (22,23) can ﬁlter, cluster and rank docking solution candidates.”
P HYSICS - INFORMED DEEP NEURAL NETWORK FOR RIGID - BODY PROTEIN DOCKING (2022, background): “…shape-complementarity of two proteins bound to each other is a well documented phenomena (Lawrence & Colman, 1993; Jones & Thornton, 1996) and has been widely used in classical methods for protein-protein docking (Gabb et al., 1997; Chen & Weng, 2002; Duhovny et al., 2002; Comeau et al., 2004).”
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers (2014, background): “…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), clustering (Comeau et al. , 2004) and symmetric multimer docking (Schneidman-Duhovny et al. , 2005).”
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, methodology): “…such as explicit side chain flexibility during docking searches, 8 use of normal mode analysis to represent protein flexibility, 9,10 clustering 11,12 or re-scoring 13 – 16 docking models to improve ranking of near-native models, and use of experimental data as restraints for docking 17 have…”
Protein–protein interaction and quaternary structure (2008, methodology): “Procedures based on that algorithm are implemented in a number of servers : ClusPro (Comeau et al. 2004), SmoothDock, MultiDock (Gabb et al. 1997), Gramm-X (Tovchigrechko & Vakser, 2006).”
The ClusPro web server for protein-protein docking (2017, background): “11,12), but since then it has been substantially modified and expanded 13–15 .”