HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

By S. D. de Vries, A. V. van Dijk, M. Krzeminski, M. V. van Dijk, A. Thureau, V. Hsu, Tsjerk A. Wassenaar, Alexandre M. J. J. Bonvin. 2007

578 citations recorded by the source corpus.

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

How researchers see this paper

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

In Computational Theory and Mathematics

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Nelly Andrusier
4. Efrat Mashiach
5. Haim J. Wolfson
6. Ruth Nussinov
7. Sjoerd Jacob de Vries
8. João P. G. L. M. Rodrigues

In Materials Chemistry

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. João P. G. L. M. Rodrigues
4. Ruth Nussinov
5. Haim J. Wolfson
6. Sjoerd Jacob de Vries
7. Nelly Andrusier
8. Efrat Mashiach

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Nelly Andrusier
4. Efrat Mashiach
5. Haim J. Wolfson
6. Ruth Nussinov
7. João P. G. L. M. Rodrigues
8. Sjoerd Jacob de Vries

Citations in the corpus

• Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions (2017, methodology): “Following the recommended default settings, HADDOCK was used to simulate 200 separate trajectories with MD refinement starting from the X-ray structure.”
• Principles of Flexible Protein-Protein Docking (2008, methodology): “For example, simulated annealing MD is used in the refinement stage of HADDOCK32,33 in order to refine the conformations of both the side-chains and the backbone.”
• Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. (2017, background): “2: HADDOCK [15, 16] can be obtained free of charge for noncommercial users by filling and returning the license form available from http://www.”
• The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (2016, methodology): “Data-driven approaches such as HADDOCK [5,6], which integrate information derived from biochemical, biophysical or bioinformatics methods to enhance sampling, scoring, or both [2], perform remarkably better.”