Data‐driven docking for the study of biomolecular complexes

By A. V. van Dijk, Rolf Boelens, Alexandre M. J. J. Bonvin. 2005

155 citations recorded by the source corpus.

Subfields: 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 Materials Chemistry

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. D. Ritchie
4. A. V. van Dijk
5. Sjoerd Jacob de Vries
6. V. Hsu
7. Rolf Boelens
8. Pedro Alexandrino Fernandes

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. D. Ritchie
4. Sjoerd Jacob de Vries
5. A. V. van Dijk
6. V. Hsu
7. Rolf Boelens
8. Pedro Alexandrino Fernandes

Citations in the corpus

• Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance (2010, methodology): “In a ‘real-life’ docking situation, AIRs are typically defined based on experimental data or interface predictions (19,20).”
• Recent progress and future directions in protein-protein docking. (2008, background): “1389-2037/08 $55.00+.00 © 2008 Bentham Science Publishers Ltd. Keywords: Protein-protein docking, protein-protein interactions, docking algorithms, data-driven docking, molecular dynamics, protein structure databases, protein interface prediction, CAPRI.”
• CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK (2011, unknown): “…in the PDB. HADDOCK has been applied to a variety of problems including protein-protein, protein-nucleic acids and protein-small molecule complexes, in combination with a wide range of experimental data, ranging from NMR, mass spectrometry to mutagenesis data (for an overview, see [9,10]).”
• Protein–ligand docking: Current status and future challenges (2006, background): “known 3D structures of its components, free or complexed with other species.(8) In terms of protein–ligand docking”
• A protein–DNA docking benchmark (2008, background): “Biomolecular docking has become a mature discipline within structural biology ( 1 ).”
• Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility (2006, methodology): “This information can be used to drive the docking (6) and limit the conformational space to be searched.”
• Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “pt From a functional point of view, docking involves the generation of an ensemble of 3D conformers of a complex starting from the known structures of its free components [7].”
• The HADDOCK web server for data-driven biomolecular docking (2010, background): “By combining this information with computational approaches such as docking, useful insights can be obtained on biomolecular interactions 1 .”