ArticleNucleic acids research2010
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- The 'very moment' when UDG recognizes a flipped-out uracil base in dsDNA.Scientific reports · 2025Article
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- The NS1 protein of influenza B virus binds 5'-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response.bioRxiv : the preprint server for biology · 2024Article
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- pyDockDNA: A new web server for energy-based protein-DNA docking and scoring.Frontiers in molecular biosciences · 2022Article
- Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.Proteins · 2020Article
- MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing.Frontiers in molecular biosciences · 2019Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- M3: an integrative framework for structure determination of molecular machines.Nature methods · 2017Article
- EMQIT: a machine learning approach for energy based PWM matrix quality improvement.Biology direct · 2017Article
- Characterization of Protein Tyrosine Phosphatase 1B Inhibition by Chlorogenic Acid and Cichoric Acid.Biochemistry · 2017Article
- Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria.Molecules (Basel, Switzerland) · 2015Review
- Promoter activation by CII, a potent transcriptional activator from bacteriophage 186.The Journal of biological chemistry · 2014Article
- Structure of bacterial transcription factor SpoIIID and evidence for a novel mode of DNA binding.Journal of bacteriology · 2014Article
- Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea.PloS one · 2014Article
- Article
- Solvated protein-DNA docking using HADDOCK.Journal of biomolecular NMR · 2013Article
- Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.Journal of biomolecular NMR · 2013Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long been challenges that prevented the development of efficient protein-DNA docking methods. We have demonstrated the ability our flexible data-driven docking method HADDOCK to deal with these before, by using custom-built DNA structural models. Here we put our method to the test on a set of 47 complexes from the protein-DNA docking benchmark. We show that HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s). Our DNA analysis and modelling procedure captures the bend and twist motions occurring upon complex formation and uses these to generate custom-built DNA structural models, more closely resembling the bound form, for use in a second docking round. We achieve throughout the benchmark an overall success rate of 94% of one-star solutions or higher (interface root mean square deviation ≤4 A and fraction of native contacts >10%) according to CAPRI criteria. Our improved protocol successfully predicts even the challenging protein-DNA complexes in the benchmark. Finally, our method is the first to readily dock multiple molecules (N > 2) simultaneously, pushing the limits of what is currently achievable in the field of protein-DNA docking.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.