HexServer: an FFT-based protein docking server powered by graphics processors
By Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, D. Ritchie. Nucleic Acids Res., 2010
647 citations recorded by the source corpus.
HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes ∼15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.
Subfields: Biophysics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/2aa2f7c3c3b2b639790c6481f4a1edca1ef87f3c
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Citations in the corpus
- HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy (2017, methodology): “…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 developed and made…”
- 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”
- Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein (2021, methodology): “After preparing the hACE2 and SARS‐CoV‐2 spike protein receptors using both full spike protein and RBD, all potentially docked molecules were analyzed using the HEX docking program.(25) Docking parameters were set as follows: Type of correlation: Only the shape dimension is 0.”
- Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment (2016, neutral): “Many employed their own docking methods, some of which were designed to handle symmetric assemblies, whereas others relied on well-established docking algorithms such as HEX,28 ZDock,29 RosettaDock,30 as well as on docking programs such as MZDock 31 which apply symmetry constraints.”
- 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”
- InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, background): “Many template-free docking servers implement a rigid-body docking approach, sometimes followed by rescoring: PatchDock (9), FireDock (10), HexServer (11), ZDOCK (12), FRODOCK 2.”