The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

By G. V. Zundert, João P. G. L. M. Rodrigues, Mikael E. Trellet, Christophe Schmitz, Panagiotis L. Kastritis, Ezgi Karaca, Adrien S. J. Melquiond, M. V. van Dijk, Sjoerd Jacob de Vries, Alexandre M. J. J. Bonvin. 2016

2,479 citations recorded by the source corpus.

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

A Comprehensive Review on Current Advances in Peptide Drug Development and Design (2019, background): “There are computational servers that have attempted to translate ambiguous experimental data into algorithmic constrains that can be applied as an option for docking [79,97].”
Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. (2017, methodology): “Moreover, the software can be used via a user-friendly web server [17, 18].”
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;”
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes (2024, positive): “4, together with an updated version of the web server that builds upon the previously described features 33 by adding support for up to 20-body docking, allowing for coarse-grained representations of proteins and DNA 34,35 by using the MARTINI forcefield 36 , supporting cryo-EM maps as restraints…”
Protein storytelling through physics (2020, neutral): “For example, Rosetta ( 45 ), Quark ( 46 ), Dock 1 ( 47 ), Cluspro ( 48 ), Haddock ( 49 ), MODELLER ( 50 ), and IMP ( 51 ) do this to outstanding effect for certain structure-based computations.”
High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio * (2016, methodology): “In the second round, the mutational data alone was incorporated as a restraint set, using each mutation as an active residue and defining passive residues within 5 Å of an active residue (44).”
Binding Affinity via Docking: Fact and Fiction (2018, methodology): “Although nowadays specific docking methods are available for distinct binding partners, such as HADDOCK for protein-protein docking [2], here we focus on the more traditional small-molecule molecular docking methods, such as GOLD [3–5], Surflex-Dock [6], AutoDock [7] and Glide [8–10], that are regul”