The HADDOCK web server for data-driven biomolecular docking

By Sjoerd Jacob de Vries, M. V. van Dijk, Alexandre M. J. J. Bonvin. Nature Protocols, 2010

1,379 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/270d44a7601739f6f92aac926a4d4edc96172989

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, background): “Developments 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 do”
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, background): “Attempts to address the limitations of computational docking have led to placing increasing focus on data-driven docking (24) and many servers now allow the user to specify interface residues and/or distance restraints, including ZDOCK, FRODOCK 2.0 (for refinement), pyDockWEB, ClusPro, GRAMM-X, Swar”
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.”
HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy (2017, background): “For years, a number of docking algorithms and their web servers such as ClusPro (10), HADDOCK (11), RosettaDock server (12), GRAMM-X (13), 3D-Garden (14), HEX server (15), SwarmDock (16), ZDOCK server (17), PatchDock (18), ATTRACT (19), pyDockSAXS (20), InterEvDock (9) and NPDock (21), have been dev”
Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. (2017, methodology): “In a data-driven approach using the program HADDOCK (de Vries et al., 2010), we used the above cross-linking and footprinting results as interaction restraints to guide the docking procedure (Table S1).”
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex (2016, methodology): “Other tools such as pepATTRACT (22) propose to prepare files to run simulations locally, or to start from 3D coordinates for the HADDOCK server (23).”
New additions to the ClusPro server motivated by CAPRI (2017, methodology): “Docking with pairwise distance restraints is fundamental to HADDOCK,22 a heavily used protein–protein docking server.”
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…”
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem (2021, methodology): “To accommodate the complexity that naturally arises from >18 years of development of new features and docking modes without compromising usability and accessibility, HADDOCK has been made freely available (with registration) to the community since 2008 via an intuitive webserver (Vries et al., 2010;”